gebhart/patrepeval huggingface dataset:
Monoclonal antibodies to reovirus reveal structure/function relationships between capsid proteins and genetics of susceptibility to antibody action (1991)

Thirteen newly isolated monoclonal antibodies (MAbs) were used to study relationships between reovirus outer capsid proteins sigma 3, mu 1c, and lambda 2 (core spike) and the cell attachment protein sigma 1. We focused on sigma 1-associated properties of serotype specificity and hemagglutination (HA). Competition between MAbs revealed two surface epitopes on mu 1c that were highly conserved between reovirus serotype 1 Lang (T1L) and serotype 3 Dearing (T3D). There were several differences between T1L and T3D sigma 3 epitope maps. Studies using T1L x T3D reassortants showed that primary sequence differences between T1L and T3D sigma 3 proteins accounted for differences in sigma 3 epitope maps. Four of 12 non-sigma 1 MAbs showed a serotype-associated pattern of binding to 25 reovirus field isolates. Thus, for reovirus field isolates, different sigma 1 proteins are associated with preferred epitopes on other outer capsid proteins. Further evidence for a close structural and functional interrelationship between sigma 3/mu 1c and sigma 1 included (i) inhibition by sigma 3 and mu 1c MAbs of sigma 1-mediated HA, (ii) enhancement of sigma 1-mediated HA by proteolytic cleavage of sigma 3 and mu 1c, and (iii) genetic studies demonstrating that sigma 1 controlled the capacity of sigma 3 MAbs to inhibit HA. These data suggest that (i) epitopes on sigma 3 and mu 1c lie in close proximity to sigma 1 and that MAbs to these epitopes can modulate sigma 1-mediated functions, (ii) these spatial relationships have functional significance, since removal of sigma 3 and/or cleavage of mu 1c to delta can enhance sigma 1 function, (iii) in nature, the sigma 1 protein places selective constraints on the epitope structure of the other capsid proteins, and (iv) viral susceptibility to antibody action can be determined by genes other than that encoding an antibody's epitope.
Intestinal cholesterol absorption efficiency in man is related to apoprotein E phenotype. (1987)

Relationship between the efficiency of cholesterol absorption and apolipoprotein E (apoE) phenotype was studied in a random sample of middle-aged Finnish men. Subjects that were either heterozygous or homozygous for the allele epsilon 2 absorbed less and synthesized more cholesterol than those with the phenotype E4/3 and E4/4, the values for the individuals with the most frequent phenotype E3/3 (56% of the population sample) falling in between. Among the whole study group, the sum of the subscripts of apoE phenotype (e.g., E2/3 = 5) was correlated positively with the fractional absorption of cholesterol (r = 0.40; P less than 0.05) and negatively with the serum level of lathosterol, a cholesterol precursor sterol reflecting the activity of cholesterol synthesis (r = -0.48; P less than 0.01). Thus, apoE polymorphism appears to affect the efficiency of cholesterol absorption and may by this mechanism contribute to the variation in plasma total and low density lipoprotein cholesterol concentration.
Isothermal Amplification and Molecular Typing of the Obligate Intracellular Pathogen Mycobacterium leprae Isolated from Tissues of Unknown Origins (2006)

Molecular diagnostic and epidemiology studies require appreciable amounts of high-quality DNA. Molecular epidemiologic methods have not been routinely applied to the obligate intracellular organism Mycobacterium leprae because of the difficulty of obtaining a genomic DNA template from clinical material. Accordingly, we have developed a method based on isothermic multiple-displacement amplification to allow access to a high-quality DNA template. In the study described in this report, we evaluated the usefulness of this method for error-sensitive, multiple-feature molecular analyses. Using test samples isolated from lepromatous tissue, we also evaluated amplification fidelity, genome coverage, and regional amplification bias. The fidelity of amplified genomic material was unaltered; and while regional differences in global amplification efficiency were seen by using comparative microarray analysis, a high degree of concordance of amplified genomic DNA was observed. This method was also applied directly to archived tissue specimens from leprosy patients for the purpose of molecular typing by using short tandem repeats; the success rate was increased from 25% to 92% without the introduction of errors. This is the first study to demonstrate that serial whole-genome amplification can be coupled with error-sensitive molecular typing methods with low-copy-number sequences from tissues containing an obligate intracellular pathogen.
The assembly and structure of the fibrin clot. (1992)

This review summarizes our current understanding of the structure of the fibrinogen molecule, its conversion to fibrin, and the main features of fibrin clot assembly and crosslinking. Several major aspects of fibrin matrix assembly and crosslinking are newly discovered, and differ significantly from more traditional views of fibrin structure. The new information that I have summarized will be of importance for correctly understanding the role that fibrin plays in the hemostatic process, and for learning how the structure of the fibrin clot network contributes to its strength, elasticity, interactions with cells, tissue matrix, and its susceptibility to fibrinolysis.
Biologic sequelae of IκB kinase (IKK) inhibition in multiple myeloma: therapeutic implications (2009)

Nuclear factor-kappaB (NF-kappaB) has an important role in multiple myeloma (MM) cell pathogenesis in the context of the bone marrow (BM) microenvironment. In NF-kappaB signaling cascades, IkappaB kinase alpha (IKKalpha) and IKKbeta are key molecules that predominantly mediate noncanonical and canonical pathways, respectively. In this study, we examined the biologic sequelae of the inhibition of IKKalpha versus IKKbeta in MM cell lines. All MM cell lines have constitutive canonical NF-kappaB activity, and a subset of MM cell lines shows noncanonical NF-kappaB activity. Adhesion to BM stromal cells further activates both canonical and noncanonical NF-kappaB activity. IKKbeta inhibitor MLN120B blocks canonical pathway and growth of MM cell lines but does not inhibit the noncanonical NF-kappaB pathway. Although IKKalpha knockdown induces significant growth inhibition in the cell lines with both canonical and noncanonical pathways, it does not inhibit NF-kappaB activation. Importantly, IKKalpha down-regulation decreases expression of beta-catenin and aurora-A, which are known to mediate MM cell growth and survival. Finally, IKKbeta inhibitor enhances the growth inhibition triggered by IKKalpha down-regulation in MM cells with both canonical and noncanonical NF-kappaB activity. Combination therapy targeting these kinases therefore represents a promising treatment strategy in MM.
Endoplasmic reticulum Ca2+-homeostasis is altered in small and non-small cell lung cancer cell lines (2009)

The significant differences in Ca2+-homeostasis between lung cancer and NHBE cells could represent a new target for cancer treatments.
Regulation of renal tubular sodium transport by cardiac natriuretic peptides: two decades of research. (2002)

This review presents the current state of our knowledge regarding the regulation of renal tubular sodium transport by natriuretic peptides, with special emphasis on recent findings in this field. Natriuretic peptides constitute a complex system involved in the regulation of sodium balance and blood pressure. The natriuretic peptide family consists of atrial peptides, such as atrial natriuretic factor (ANF, ANP(99-126)), long-acting natriuretic peptide (ANP(1-30)), vessel dilator (ANP(31-67)) and kaliuretic peptide (ANP(79-98)), as well as brain or B-type natriuretic peptide (BNP), C-type natriuretic peptide (CNP) and urodilatin. Natriuretic peptides act on target cells through A-type and B-type receptors and stimulate cyclic GMP synthesis. ANF stimulates natriuresis mainly by inhibiting sodium reabsorption in the inner medullary collecting duct. The effect results from coordinate inhibition of apical sodium channels and basolateral Na+, K+-ATPase. Additional effects on sodium transport occur in more proximal nephron segments and on glomerular filtration when hormone concentration is elevated. BNP and urodilatin share the same mechanism of action. CNP synthetized in several nephron segments acts through specific B-type natriuretic peptide receptors, which are also expressed in renal tubule, but have a different distribution than A-type receptors. ANP(1-30), ANP(31-67) and ANP(79-98) decrease Na+, K+-ATPase activity in tubular cells through a prostaglandin E2-dependent mechanism.
A hierarchical approach to all‐atom protein loop prediction (2004)

The application of all-atom force fields (and explicit or implicit solvent models) to protein homology-modeling tasks such as side-chain and loop prediction remains challenging both because of the expense of the individual energy calculations and because of the difficulty of sampling the rugged all-atom energy surface. Here we address this challenge for the problem of loop prediction through the development of numerous new algorithms, with an emphasis on multiscale and hierarchical techniques. As a first step in evaluating the performance of our loop prediction algorithm, we have applied it to the problem of reconstructing loops in native structures; we also explicitly include crystal packing to provide a fair comparison with crystal structures. In brief, large numbers of loops are generated by using a dihedral angle-based buildup procedure followed by iterative cycles of clustering, side-chain optimization, and complete energy minimization of selected loop structures. We evaluate this method by using the largest test set yet used for validation of a loop prediction method, with a total of 833 loops ranging from 4 to 12 residues in length. Average/median backbone root-mean-square deviations (RMSDs) to the native structures (superimposing the body of the protein, not the loop itself) are 0.42/0.24 A for 5 residue loops, 1.00/0.44 A for 8 residue loops, and 2.47/1.83 A for 11 residue loops. Median RMSDs are substantially lower than the averages because of a small number of outliers; the causes of these failures are examined in some detail, and many can be attributed to errors in assignment of protonation states of titratable residues, omission of ligands from the simulation, and, in a few cases, probable errors in the experimentally determined structures. When these obvious problems in the data sets are filtered out, average RMSDs to the native structures improve to 0.43 A for 5 residue loops, 0.84 A for 8 residue loops, and 1.63 A for 11 residue loops. In the vast majority of cases, the method locates energy minima that are lower than or equal to that of the minimized native loop, thus indicating that sampling rarely limits prediction accuracy. The overall results are, to our knowledge, the best reported to date, and we attribute this success to the combination of an accurate all-atom energy function, efficient methods for loop buildup and side-chain optimization, and, especially for the longer loops, the hierarchical refinement protocol.
Spectral Signatures Of Chemical Agents And Simulants (1985)

A summary of the current status of spectral information on chemical agents, their spectral simulants, and possible field interferents is presented along with comments on current programs being used to expand this spectral data base. The current programs include the collection of Raman and near-infrared spectra and various methods of obtaining the real and imaginary refractive indices (primarily in the mid-infrared spectral region). All of the spectral information will be directly accessible to qualified users on the U.S. Army Chemical Research and Development Center's Univac computer.
Leveraging StoLPaN host environment for portable diagnostic health-care platform. (2008)

This paper reports on leveraging our recent achievement in StoLPaN project that combines mobile phones/PDAs with the Near Field Communication (NFC) wireless technology to further support a portable diagnostic health care platform (namely POCEMON).
Essential role of mitochondrial energy metabolism in Foxp3 + T‐regulatory cell function and allograft survival (2015)

Conventional T (Tcon) cells and Foxp3(+) T-regulatory (Treg) cells are thought to have differing metabolic requirements, but little is known of mitochondrial functions within these cell populations in vivo. In murine studies, we found that activation of both Tcon and Treg cells led to myocyte enhancer factor 2 (Mef2)-induced expression of genes important to oxidative phosphorylation (OXPHOS). Inhibition of OXPHOS impaired both Tcon and Treg cell function compared to wild-type cells but disproportionally affected Treg cells. Deletion of Pgc1α or Sirt3, which are key regulators of OXPHOS, abrogated Treg-dependent suppressive function and impaired allograft survival. Mef2 is inhibited by histone/protein deacetylase-9 (Hdac9), and Hdac9 deletion increased Treg suppressive function. Hdac9(-/-) Treg showed increased expression of Pgc1α and Sirt3, and improved mitochondrial respiration, compared to wild-type Treg cells. Our data show that key OXPHOS regulators are required for optimal Treg function and Treg-dependent allograft acceptance. These findings provide a novel approach to increase Treg function and give insights into the fundamental mechanisms by which mitochondrial energy metabolism regulates immune cell functions in vivo.
Template-Directed Adsorption of Block Copolymers on Alkanethiol-Patterned Gold Surfaces (2006)

Functionalized alkanethiols have been self-assembled on gold to modify the wetting properties of the surface and promote or hinder the adsorption of block copolymers containing both hydrophobic and hydrophilic blocks. X-ray photoelectron spectroscopy (XPS) studies of spin-coated polyethylene-block-poly(ethylene oxide) (PE-b-PEO) copolymers on 16-mercaptohexadecanoic acid (MHDA)-, octadecanethiol (ODT)-, and 1H,1H,2H,2H-perfluorodecanethiol (PFDT)-covered surfaces have been performed. In the case of an 80 wt % PEO block copolymer, spin-coating on a gold surface precovered with MHDA results in a polymer film thick enough to completely attenuate Au 4f photoelectrons; spin-coating on the more hydrophobic ODT and PFDT monolayers leads to significantly thinner polymer films and incomplete attenuation of the gold photoelectrons. The opposite results are observed when a 20 wt % PEO block copolymer is used. Angle-resolved XPS studies of the 80 wt % PEO block copolymer spin-coated onto an MHDA-covered surface indicate that the PE blocks of the polymer segregate to the near-surface region, oriented away from the hydrophilic carboxylic acid tails of the monolayers; the surface concentration of PE is further enhanced by annealing at 90 degrees C. Microcontact printing and dip-pen nanolithography have been used to pattern gold surfaces with MHDA, and the surfaces have been backfilled with ODT or PFDT, such that the unpatterned regions of the surface are covered with hydrophobic monolayers. In the case of backfilling with PFDT, spin-coating the 80 wt % PEO copolymer onto these patterned surfaces and subsequent annealing results in the block copolymer preferentially adsorbing on the MHDA-covered regions and forming well-defined patterns that mimic the MHDA pattern, as determined by scanning electron microscopy and atomic force microscopy. Significantly worse patterning, characterized by micron-sized polymer droplets, results when the surface is backfilled with ODT instead of PFDT. Using PFDT and MHDA, polymer features having widths as small as 500 nm have been formed. These studies demonstrate a novel method to pattern block copolymers with nanoscale resolution.
Quality-adaptive Prefetching for Interactive Branched Video using HTTP-based Adaptive Streaming (2014)

Interactive branched video that allows users to select their own paths through the video, provides creative content designers with great personalization opportunities; however, such video also introduces significant new challenges for the system developer. For example, without careful prefetching and buffer management, the use of multiple alternative playback paths can easily result in playback interruptions. In this paper, we present a full implementation of an interactive branched video player using HTTP-based Adaptive Streaming (HAS) that provides seamless playback even when the users defer their branch path choices to the last possible moment. Our design includes optimized prefetching policies that we derive under a simple optimization framework, effective buffer management of prefetched data, and the use of parallel TCP connections to achieve efficient buffer workahead. Through performance evaluation under a wide range of scenarios, we show that our optimized policies can effectively prefetch data of carefully selected qualities along multiple alternative paths such as to ensure seamless playback, offering users a pleasant viewing experience without playback interruptions.
Electromagnetic modelling of current flow in the heart from TASER devices and the risk of cardiac dysrhythmias (2007)

Increasing use by law enforcement agencies of the M26 and X26 TASER electrical incapacitation devices has raised concerns about the arrhythmogenic potential of these weapons. Using a numerical phantom constructed from medical images of the human body in which the material properties of the tissues are represented, computational electromagnetic modelling has been used to predict the currents arising at the heart following injection of M26 and X26 waveforms at the anterior surface of the chest (with one TASER 'barb' directly overlying the ventricles). The modelling indicated that the peak absolute current densities at the ventricles were 0.66 and 0.11 mA mm(-2) for the M26 and X26 waveforms, respectively. When applied during the vulnerable period to the ventricular epicardial surface of guinea-pig isolated hearts, the M26 and X26 waveforms induced ectopic beats, but only at current densities greater than 60-fold those predicted by the modelling. When applied to the ventricles in trains designed to mimic the discharge patterns of the TASER devices, neither waveform induced ventricular fibrillation at peak currents >70-fold (for the M26 waveform) and >240-fold (for the X26) higher than the modelled current densities. This study provides evidence for a lack of arrhythmogenic action of the M26 and X26 TASER devices.
Short-lasting nicotinic and long-lasting muscarinic depolarizing responses of thalamocortical neurons to stimulation of mesopontine cholinergic nuclei (1991)

1. The responses of thalamocortical neurons to stimulation of mesopontine [peribrachial (PB) and laterodorsal (LDT)] cholinergic nuclei were studied intracellularly in urethan-anesthetized cats. Neurons recorded from anterior thalamic (AT), ventroanterior-ventrolateral (VA-VL) and rostral intralaminar centrolateral (CL) nuclei were physiologically identified by their orthodromic responses to prethalamic stimulation and/or antidromic activation from the cerebral cortex. 2. Besides early excitatory and inhibitory postsynaptic potentials (EPSPs and IPSPs) that were not sensitive to cholinergic antagonists, two types of cholinergic responses were elicited by PB/LDT stimulation: a short-lasting and a late, long-lasting depolarization. All these components survived monoamine depletion by reserpine. 3. The latency of the short-lasting depolarizing response was 147.4 +/- 27.3 (SE) ms. The response lasted for 1.3 +/- 0.1 s and had a peak amplitude of 4.2 +/- 0.3 mV. This component was associated with 10-30% increase in membrane conductance and was abolished by systemic administration of the nicotinic antagonist mecamylamine. 4. The long-lasting depolarizing response had a latency of 1.2 +/- 0.1 s, a duration of 20.8 +/- 2.2 s, and a peak amplitude of 5.4 +/- 0.4 mV. Similar values were found in decorticated animals. The duration and amplitude of the late depolarizing component were dependent on stimulation parameters and membrane potential. This response increased under depolarizing current, decreased and eventually disappeared under hyperpolarizing current, and was associated on average with 40% increase in apparent input resistance. After systemic administration of the muscarinic antagonist scopolamine, the long-lasting depolarization disappeared; the surviving short-lasting depolarization was subsequently abolished by mecamylamine. 5. The prolonged depolarizing response of thalamocortical neurons to mesopontine cholinergic stimulation was accompanied by a desynchronization of the electroencephalogram (EEG). These two phenomena had a similar time course. Stimulation of deep cerebellar nuclei, whose axons traverse the PB area, did not induce a long-lasting depolarization of target thalamic cells, nor an EEG desynchronization. 6. These data demonstrate that, in addition to an initial nicotinic excitation, brain stem cholinergic stimulation elicits a late, long-lasting muscarinic depolarization of thalamocortical neurons. We suggest that the prolonged depolarization plays an important role in cortical activation.
Immunodiffusion Analysis of Yaba Poxvirus Structural and Associated Antigens (1970)

Yaba poxvirus virions were extracted and purified from Rhesus monkey tumors. A saline-soluble virion fraction (Y-xp), obtained by mechanical fractionation of purified virions with an X-press, contained seven components in acrylamide gel electrophoresis; five of these components were reactive in immunodiffusion with whole virion and Y-xp antisera produced in rabbits and monkeys. The saline-insoluble residue remaining after X-press treatment was hydrolyzed with sodium dodecyl sulfate, urea, and 2-mercaptoethanol (SUM). This fraction, Y-sum, contained five components, four of which were demonstrable by immunodiffusion. There was no evidence of antigenic relationships between Y-xp and Y-sum antigens in immunodiffusion. In acrylamide gel electrophoresis, one Y-xp and one Y-sum component had similar mobilities. Y-xp but not Y-sum antisera contained viral-neutralizing antibodies. Virus-free saline extracts of Yaba tumor prepared with Genetron (YS) were essentially devoid of virion structural antigens. They failed to induce precipitating antibodies for virion antigens, were nonreactive in immunodiffusion with virion antisera, and gave low complement-fixation titers with virion antisera. Yaba virion antigens were recovered from the Genetron tumor sediment by SUM and alkaline hydrolysis. Antisera prepared to YS extracts gave a maximum of 17 precipitin lines in immunodiffusion with YS extracts; none was identified as a virion structural antigen. Saline extracts of tumor prepared without Genetron contained immunogenic amounts of 5 virion antigens and 12 to 14 associated antigens. Animals immunized with infected cell culture extracts (virus-free) formed antibodies to six to seven virion antigens. The implications of using extracts of Yaba poxvirus-infected tissues in complement-fixation tests to measure virion antibodies were discussed.