gebhart/patrepeval huggingface dataset:
Interplay between Chain Collapse and Microphase Separation in Bottle-Brush Polymers with Two Types of Side Chains (2010)

Conformations of a bottle-brush polymer with two types (A,B) of grafted side chains are studied by molecular dynamics simulations, using a coarse-grained bead−spring model with side chains of up to N = 50 effective monomers. Varying the solvent quality and the grafting density, the crossover from the "pearl-necklace" structure to dense cylinders is studied. Whereas for small grafting density, A- and B-chains form separate collapsed chains, at intermediate grafting density, larger "pearls" containing several chains are observed, exhibiting microphase separation between A and B in "dumbbell"-type configurations. At still larger grafting density, short-range order of "Janus dumbbell"-type is observed. It is argued that because of the quasi-1D character of bottle-brush polymers with stiff backbones, all phase changes occur gradually, and no sharp-phase transitions like in bulk polymer mixtures or block copolymer melts can be observed.
An obstacle avoidance scheme for hyper-redundant manipulators-global motion planning in posture space (2002)

A hyper redundant manipulator has a very large or infinite degree of kinematic redundancy, thus it is possessed of unconventional features such as the ability to enter a narrow space while avoiding obstacles. We propose a novel obstacle avoidance technique for the hyper redundant manipulator to perform a payload location task from point to point while avoiding existing static obstacles in the environment. The scheme is based on analysis in the defined posture space, where three parameters were used to determine the hyper redundant manipulator configurations. The scheme is verified by computer simulation in case of using the model of the developed Hyper-R Arm. It shows that our method works perfect and the obstacles are well avoided globally.
Spinal cord oligodendrocytes develop from ventrally derived progenitor cells that express PDGF alpha-receptors (1996)

Platelet-derived growth factor alpha-receptors (PDGFR alpha) are expressed by a subset of neuroepithelial cells in the ventral half of the embryonic day 14 (E14) rat spinal cord. The progeny of these cells subsequently proliferate and migrate into the dorsal parts of the cord after E16. Here, we show that E14 ventral cells are able to generate oligodendrocytes in culture but that dorsal cells acquire this ability only after E16, coinciding with the appearance of PDGFR alpha-immunoreactive cells in the starting population. PDGFR alpha-positive cells in optic nerve and spinal cord cultures co-labelled with antibody markers of oligodendrocyte progenitors. When PDGFR alpha-positive cells were purified from embryonic rat spinal cords by immunoselection and cultured in defined medium, they all differentiated into oligodendrocytes. Very few oligodendrocytes developed in cultures of embryonic spinal cord cells that had been depleted of PDGFR alpha-expressing cells by antibody-mediated complement lysis. These data demonstrate that all PDGFR alpha-positive cells in the embryonic rat spinal cord are oligodendrocyte progenitors and that most or all early-developing oligodendrocytes are derived from these ventrally-derived precursors.
Interior near-field acoustical holography in flight (2000)

In this paper boundary element methods (BEM) are mated with near-field acoustical holography (NAH) in order to determine the normal velocity over a large area of a fuselage of a turboprop airplane from a measurement of the pressure (hologram) on a concentric surface in the interior of the aircraft. This work represents the first time NAH has been applied in situ, in-flight. The normal fuselage velocity was successfully reconstructed at the blade passage frequency (BPF) of the propeller and its first two harmonics. This reconstructed velocity reveals structure-borne and airborne sound-transmission paths from the engine to the interior space.
Audio/Video Synchronization in Compressed Systems - A Status Report (2009)

Audio/Video synchronization (“Lip-sync”) is an ongoing problem in digital multimedia broadcasting. This paper will review some of the sources of the problem (end to end in the system), as well as current work towards resolving it being undertaken by different organizations (SMPTE, IEC, EBU, ATSC, CEA, …) worldwide. A new CEA “CEB-20” which provides detailed decoder implementation guidance will be reviewed in detail. The work of the current SMPTE Study Group will also be reviewed.
The Perils of Personhood (1988)

In the abortion debate, one of the more overworked arguments concerns the if and when of the humanity of a fetus. For those who argue along these lines, the answer to these questions guarantees a resolution of the entire abortion issue. Thus, if the fetus is human, it must not be aborted except when the mother's life is endangered (and, for some, not even then): but if it is not human, it may be aborted under any circumstances.KeywordsMoral AgentPublic AffairHuman HappinessPotential PersonHuman VegetableThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Axis determination by inhibition of Wnt signaling in Xenopus (1999)

The Wnt family of secreted polypeptides participate in a variety of developmental processes in which embryonic polarity is established. To study a role for Wnt ligands in vertebrate axis determination, we interfered with Wnt signaling in the embryo using the extracellular domain of Xenopus Frizzled 8 (ECD8), which blocks Wnt-dependent activation of a target gene in Xenopus ectodermal explants. Expression of ECD8 in ventral blastomeres resulted in formation of secondary axes containing abundant notochord and head structures. These results suggest that Wnt signaling is required to maintain ventral cell fates and has to be suppressed for dorsal development to occur.
Cell surface anchorage and ligand-binding domains of the Saccharomyces cerevisiae cell adhesion protein alpha-agglutinin, a member of the immunoglobulin superfamily. (1993)

alpha-Agglutinin is a cell adhesion glycoprotein expressed on the cell wall of Saccharomyces cerevisiae alpha cells. Binding of alpha-agglutinin to its ligand a-agglutinin, expressed by a cells, mediates cell-cell contact during mating. Analysis of truncations of the 650-amino-acid alpha-agglutinin structural gene AG alpha 1 delineated functional domains of alpha-agglutinin. Removal of the C-terminal hydrophobic sequence allowed efficient secretion of the protein and loss of cell surface attachment. This cell surface anchorage domain was necessary for linkage to a glycosyl phosphatidylinositol anchor. A construct expressing the N-terminal 350 amino acid residues retained full a-agglutinin-binding activity, localizing the binding domain to the N-terminal portion of alpha-agglutinin. A 278-residue N-terminal peptide was inactive; therefore, the binding domain includes residues between 278 and 350. The segment of alpha-agglutinin between amino acid residues 217 and 308 showed significant structural and sequence similarity to a consensus sequence for immunoglobulin superfamily variable-type domains. The similarity of the alpha-agglutinin-binding domain to mammalian cell adhesion proteins suggests that this structure is a highly conserved feature of adhesion proteins in diverse eukaryotes.
BNP‐Guided Therapy Not Better Than Expert's Clinical Assessment for β‐Blocker Titration in Patients With Heart Failure (2005)

B-type natriuretic peptide (BNP) is a cardiac neurohormone used as a noninvasive tool for diagnosing and monitoring heart failure. Beta blockers have beneficial effects in patients with heart failure as well as a direct effect on BNP plasma levels. The aim of this study is to compare the efficacy of a BNP-guided approach vs. standard care on beta-blocker titration in heart failure patients. Forty-one patients with heart failure were randomized into a clinical trial. Bisoprolol was started, and the dose was regularly up-titrated. BNP was measured monthly. The clinical group had beta-blocker dosage increased according to standard care, whereas the BNP group had beta-blocker dosage up-titrated according to plasma BNP levels plus standard care. The primary outcome was mean beta-blocker dose achieved after 3 months. BNP levels, left ventricular ejection fraction, clinical score, quality of life, and hospitalization were collected in all patients. BNP-guided up-titration of beta blocker in ambulatory patients with heart failure did not result in higher doses of beta blocker at the end of 3 months+/-SD (5.9+/-4.3 mg vs. 4.4+/-3.4 mg, p=0.22). Left ventricular ejection fraction was significantly improved in both groups by 7.3% (95% confidence interval, 4.1%-10.4%; p<0.0001). A trend toward better quality of life was seen in the BNP group.
Evidence for specificity in the encapsidation of Sindbis virus RNAs (1989)

We investigated the interaction of the capsid protein of Sindbis virus with Sindbis viral RNAs and defined a region of the genome that is required for binding in vitro and for packaging in vivo. The binding studies were performed with purified capsid protein immobilized on nitrocellulose and 32P-labeled RNAs transcribed in vitro from viral and nonspecific cDNAs. Genomic and defective interfering (DI) RNAs bound capsid protein significantly better than either the subgenomic (26S) RNA or nonspecific RNAs. Transcripts prepared from either truncated or deleted cDNAs were used to define the segment required for binding. This segment, which is represented twice in DI RNA, lies between nucleotides 746 and 1226 of the genomic RNA and is within the coding region of the nonstructural protein nsP1. Insertion of a domain covering these sequences into a nonviral RNA was able to convert it from a background level of binding to an activity that was 80% that of the Sindbis virus DI RNA. We analyzed DI RNA transcripts in detail because they could be studied not only for the ability to bind capsid protein in vitro but also for the ability to be replicated and packaged in vivo in the presence of helper virion RNA. The results obtained with three DI RNAs are reported. One (CTS14), which has one copy of the binding domain, bound efficiently to capsid protein in vitro and was packaged in vivo as measured by amplification on passaging. In contrast, a DI RNA (CTS1) which lacked this region did not bind to capsid protein and was not detected on passaging. By using lipofectin (P. L. Felgner, T. R. Gadek, M. Holm, R. Roman, H. W. Chan, M. Wenz, J.P. Northrop, G. M. Ringold, and M. Danielson, Proc. Natl. Acad. Sci. USA 84:7413-7417, 1987) to enhance RNA uptake, we were able to demonstrate that CTS1 RNA was replicated in the transfected cells. It was replicated to the same level as another DI RNA (CTS253) which has only the 3' 279 nucleotides of the binding domain and these are located near the 3' terminus of the RNA. CTS253 bound capsid protein to an intermediate level but was amplified on passaging. The binding studies and the in vivo packaging data, taken together, provide strong support for the conclusion that there is a specific capsid recognition domain in Sindbis virus RNA that plays a role in nucleocapsid assembly.
Ockham's Razor and Selective Androgen Receptor Modulators (SARMs): Are We Overlooking the Role of 5 -Reductase? (2007)

Selective Androgen Receptor Modulators (SARMs) are a novel class of AR ligands that possess tissue-selective pharmacological activities. SARMs of various chemical structures have been discovered and characterized, and lead compounds with much improved specificity for AR, in vivo pharmacokinetic profiles, and higher degree of tissue selectivity have entered clinical development, and are expected to dramatically expand the clinical applications of androgens. With the rapid progress in SARM discovery and increasing demand for mechanism-based drug design, more and more research efforts have been devoted to the mechanisms of action of the observed tissue selectivity of SARMs. There is increasing enthusiasm in adapting the molecular mechanisms of action from SERM research to the SARM field; however, is the SARM story really so complicated? The tissue-specific expression of 5alpha-reductase might provide a simple explanation for this puzzle.
Collaborative multi-robot exploration (2002)

In this paper we consider the problem of exploring an unknown environment by a team of robots. As in single-robot exploration the goal is to minimize the overall exploration time. The key problem to be solved therefore is to choose appropriate target points for the individual robots so that they simultaneously explore different regions of their environment. We present a probabilistic approach for the coordination of multiple robots which, in contrast to previous approaches, simultaneously takes into account the costs of reaching a target point and the utility of target points. The utility of target points is given by the size of the unexplored area that a robot can cover with its sensors upon reaching a target position. Whenever a target point is assigned to a specific robot, the utility of the unexplored area visible from this target position is reduced for the other robots. This way, a team of multiple robots assigns different target points to the individual robots. The technique has been implemented and tested extensively in real-world experiments and simulation runs. The results given in this paper demonstrate that our coordination technique significantly reduces the exploration time compared to previous approaches.
Metal binding properties and secondary structure of the zinc-binding domain of Nup475 (1996)

Nup475 is a nuclear zinc-binding protein of unknown function that is induced in mammalian cells by growth factor mitogens. Nup475 contains two tandemly repeated sequences YKTELCX8CX5CX3H (Cys3His repeats) that are thought to be zinc-bindin domains. Similar sequences have been found in a number of proteins from various species of eukaryotes. To determine the metal binding properties and secondary structure of the putative zinc-binding domains of Nup475, we have used synthetic or recombinant peptides that contain one or two domain sequences. The peptide with a single domain bound 1.0 +/- 0.1 equivalents of Co2+, and the peptide with two domains bound 1.7 +/- 0.4 equivalents of Co2+. Both peptides bound Co2+ and Zn2+ with affinities similar to those of classical zinc finger peptides. In each case, the Co2+ complex exhibited strong d-d transitions characteristic of tetrahedral coordination. For structural studies by nuclear magnetic resonance spectroscopy, we used a more soluble two-domain peptide that had a single amino acid substitution in a nonconserved amino acid residue in the second Cys3His repeat. The mutant peptide unexpectedly showed loss of one of its metal binding sites and displayed ordered structure for only the first Cys3His sequence. On the basis of the nuclear magnetic resonance data, we propose a structure for the Nup475 metal-binding domain in which the zinc ion is coordinated by the conserved cysteines and histidine, and the conserved YKTEL motif forms a parallel sheet-like structure with the C terminus of this domain. This structure is unlike that of any previously described class of metal binding domain.
D1- Versus D2-Receptor Modulation of Visuospatial Working Memory in Humans (1998)

The effects of pergolide, a mixed D1/D2 receptor agonist, and bromocriptine, a selective D2 receptor agonist, were assessed in a visual delay task to further investigate the "dopamine link" of working memory in humans and to look for differential D1 versus D2 receptor contributions. Two groups of 32 healthy young adults (16 female) received either 0.1 mg of pergolide or 2.5 mg of bromocriptine in a placebo-controlled cross-over design. A pretreatment with domperidone, a peripherally active D2 antagonist, was performed in both groups to reduce side effects. Interindividual differences in pharmacokinetics were controlled by the time course of serum prolactin inhibition. The working memory paradigm was a visuospatial delayed matching task; the location of a randomly generated seven-point pattern had to be memorized and compared after 2, 8, or 16 sec with a second pattern that was either identical or slightly shifted within a reference frame. The task was designed with the intention to present unique stimuli at each trial and to require minimal motor demands. Practice effects between the two pharmacological test days were minimized by training sessions that preceded the tests. The paradigm showed significant error and reaction time increases with longer delays. After comparable doses, only pergolide, but not bromocriptine, facilitated visuospatial working memory performance as demonstrated by a significant drug-by-delay interaction. These findings are in accordance with the monkey literature as well as with neuroanatomical findings, and they confirm a preferential role of prefrontal D1 receptors for working memory modulation in humans.
Expression of heterologous genes in oncolytic adenoviruses using picornaviral 2A sequences that trigger ribosome skipping (2008)

Insertion of picornaviral 2A sequences into mRNAs causes ribosomes to skip formation of a peptide bond at the junction of the 2A and downstream sequences, leading to the production of two proteins from a single open reading frame. Adenoviral protein IX is a minor capsid protein that has been used to display foreign peptides on the surface of the capsid. We have used 2A sequences from the foot-and-mouth disease virus (FMDV) and porcine teschovirus 1 (PTV-1) to express protein IX (pIX) and green fluorescent protein (GFP) from pIX-2A-GFP fusion genes in an oncolytic virus derived from human adenovirus 5. GFP was efficiently expressed by constructs containing either 2A sequence. Peptide bond skipping was more efficient with the 58 aa FMDV sequence than with the 22 aa PTV-1 2A sequence, but the virus with the FMDV 2A sequence showed a reduction in plaque size, cytopathic effect, viral burst size and capsid stability. We conclude that ribosome skipping induced by 2A sequences is an effective strategy to express heterologous genes in adenoviruses; however, careful selection or optimization of the 2A sequence may be required if protein IX is used as the fusion partner.
Effect of Three Resistant Soybean Genotypes on the Fecundity, Mortality, and Maturation of Soybean Aphid (Homoptera: Aphididae) (2004)

The fecundity, longevity, mortality, and maturation of the soybean aphid, Aphis glycines Matsumura (Homoptera: Aphididae), were characterized using three resistant soybean, Glycine max (L.) Merrill, genotypes ('Dowling', 'Jackson', and PI200538 'Sugao Zarai') and two susceptible genotypes ('Pana' and 'Loda'). Antibiosis in the resistant genotypes was demonstrated by a significant decrease in fecundity and longevity and increased mortality of A. glycines. Aphid fecundity, measured as number of offspring produced in the first 10 d by each viviparous aptera, was higher on Pana than on the resistant genotypes. Aphid longevity, the mean number of days a 1-d-old adult lived, was 7 d longer on Pana than on Dowling and Jackson. The mortality of both viviparous apterae and nymphs on resistant genotypes was significantly higher than on susceptible genotypes. A greater number of first instars survived to maturation stage (date of first reproduction) on susceptible plants than on resistant plants. None of the first instars placed on Dowling and PI200538 leaves survived to maturation. Observations of aphid behavior on leaves indicated that aphids departed from the leaves of resistant plants 8-24 h after being placed on them, whereas they remained indefinitely on leaves of susceptible cultivars and developed colonies. Reduced feeding due to ingestion of potentially toxic compounds in soybean may explain the possible mechanism of resistance to the soybean aphid.
Complete primary structures of two major murine serum amyloid A proteins deduced from cDNA sequences. (1985)

cDNA clones encoding two major mouse serum amyloid A proteins, SAA1 and SAA2, were isolated from a liver cDNA library of the lipopolysaccharide-stimulated BALB/c mouse, and their nucleotide sequences were determined. The insert of the SAA2 cDNA clone contained 607 nucleotides with a 5' untranslated region of 36 nucleotides, a signal peptide region corresponding to 19 amino acids, a mature protein region corresponding to 103 amino acids, and a 3' untranslated region of 202 nucleotides. The SAA1 cDNA insert contained 549 nucleotides specifying a part of a signal peptide region, a mature protein region, and a 3' untranslated region. A comparison of the nucleotide and deduced amino acid sequences of SAA1 cDNA with that of SAA2 cDNA showed a high degree of homology: 95% nucleotide sequence homology in the coding region (91% amino acid sequence homology) and 90% homology in the 3' untranslated region. One of nine amino acid differences between SAA1 and SAA2 predicted from the cDNA sequences was located in a putative proteolytic cleavage site for amyloid A protein formation: SAA2 had the Thr-Met sequence in this site, while SAA1 had the Thr-Ile sequence. This suggests that SAA1, which does not deposit as amyloid A protein, is also potentially susceptible to putative proteolytic enzymes. In addition, as compared with mouse SAA2, human SAA1, monkey and mink amyloid A protein, mouse SAA1 had two unique substitutions, which may play a role in differential deposition of mouse SAA isotypes in amyloid tissues.
Estimation of kerogen porosity in source rocks as a function of thermal transformation: Example from the Mowry Shale in the Powder River Basin of Wyoming (2012)

Evaluations of porosity relevant to hydrocarbon storage capacity in kerogen-rich mudrocks (i.e., source rocks) have thus far been plagued with ambiguity, in large part because conventional core and petrophysical techniques were not designed for this rock type. The growing recognition of an intraparticle organic nanopore system that is related to thermal maturity is beginning to clarify this ambiguity. This mode of porosity likely evolved with the thermal transformation of labile kerogen and probably neither depends nor interacts (except perhaps chemically) with previously assumed matrix or mineral porosity that is dominated by bound water, and that may be largely irrelevant to hydrocarbon storage capacity in these rocks. To address this newly recognized and important nonmatrix kerogen pore system, that is arguably the dominant hydrocarbon storage and mobility network in these rocks, we introduce a relatively simple kinetic model that describes porosity development within kerogen as a function of thermal maturation. Kerogen porosity development is estimated within the upper Albian Mowry Shale in the Powder River Basin of Wyoming to illustrate the approach. Relevant storage capacity is considered to have evolved with thermal decomposition of organic matter during catagenesis, where we estimate that kerogen porosity does not typically exceed 3% of bulk rock volume. Modeled oil-in-place estimates are comparable to residual oil estimates from pyrolysis data (S1) at lower maturities, but exceed pyrolytic S1 yields at higher maturities. We hypothesize, therefore, that a subsurface kinetic porosity model might represent a means to account for S1 losses at surface conditions and to circumvent difficulties surrounding estimations of expulsion efficiencies that are inherent to more traditional mass balance calculations.