gebhart/patrepeval huggingface dataset:
The Na+ Binding Site of Thrombin (1995)

Thrombin is an allosteric serine protease existing in two forms, slow and fast, targeted toward anticoagulant and procoagulant activities. The slow --> fast transition is induced by Na+ binding to a site contained within a cylindrical cavity formed by three antiparallel beta-strands of the B-chain (Met180-Tyr184a, Lys224-Tyr228, and Val213-Gly219) diagonally crossed by the Glu188-Glu192 strand. The site is shaped further by the loop connecting the last two beta-strands and is located more than 15 A away from the catalytic triad. The cavity traverses through thrombin from the active site to the opposite surface and contains Asp189 of the primary specificity site near its midpoint. The bound Na+ is coordinated octahedrally by the carbonyl oxygen atoms of Tyr184a, Arg221a, and Lys224, and by three highly conserved water molecules in the D-Phe-Pro-Arg chloromethylketone thrombin. The sequence in the Na+ binding loop is highly conserved in thrombin from 11 different species and is homologous to that found in other serine proteases involved in blood coagulation. Mutation of two Asp residues flanking Arg221a (D221A/D222K) almost abolishes the allosteric properties of thrombin and shows that the Na+ binding loop is also involved in direct recognition of protein C and antithrombin.
Detection of Rotavirus Types G8 and G10 among Brazilian Children with Diarrhea (1998)

Characterization of 49 rotavirus-positive stool specimens from children with diarrhea in the state of Rio de Janeiro, Brazil, in 1996 and 1997 revealed a great diversity of rotavirus G types. Conventional types G1 and G3 accounted for 27 and 12% of the infections, respectively, whereas 60% of the infections were caused by unconventional types G5 (25%), G10 (16%), and G8 (4%) and mixed G types (16%).
Root and Shoot Characteristics of Peach Trees with Different Growth Habits (2001)

Shoot and root characteristics of four peach tree [ Prunus persica (L.) Batsch (Peach Group)] growth habits (compact, dwarf, pillar, and standard) were studied. In compact trees, leaf number (1350/tree) was twice, but leaf area (6 cm 2 /leaf) was half that of pillar and standard trees. The number of lateral branches in compact trees (34) was nearly three times more than in pillar and standard trees. Leaf area index (total one-side leaf area per tree divided by the canopy cross-sectional area of the tree) of pillar trees was greater than compact, dwarf, and standard trees (13 compared with 4, 4, and 3, respectively) due to a narrower crown diameter. Dwarf trees were distinct with few leaves (134/tree) and less than half the roots of the other growth habits. Compact trees produced more higher order lateral (HOL) roots than pillar and standard trees. More second order lateral (SOL) roots were produced by compact than standard trees (1.2 vs. 0.8 SOL roots per centimeter first order lateral root). Pillar trees had higher shoot: root dry weight (DW) ratios (2.4) than compact and standard trees (1.7 for both) due to lower root DWs. Root topology was similar among compact, pillar, and standard peach trees but root axes between branch junctions (links) were significantly longer in compact trees. Compact trees had more and longer HOL roots in roots originating near the root collar (stem-root junction) (i.e., more fibrous roots) and this appeared to correlate with more lateral branches in the canopy. These results indicate significant differences in root as well as shoot architecture among growth habits that can affect their use as scion or rootstock cultivars.
NEUTROPHILS (2006)

Neutrophils represent critical components of the innate immune system that bear primary responsibility for phagocytosis and killing of invading pathogens. We have reported that neutrophils are the main source of anti-inflammatory mediators in whole blood. This study determined if neutrophils could regulate cytokine levels under cell-mixing conditions. Neutrophils (PMN) and mononuclear cells (MC) were isolated from peripheral blood. PMN (50 × 105/ml) and MC (1 to 5 × 105 cell/ml) were either cultured separately or co-cultured at 37°C with 5% CO2 in RPMI-1640 with 5% autologous plasma. The cells were stimulated with 50 ng/ml of LPS for 24 h. As shown in Table 1, pro-inflammatory cytokines were produced by MC but not PMN. With the exception of IL-8, no detectable TNF-α, IL-1β or IL-6 was found in stimulated PMNs. In contrast, PMNs were an important source of anti-inflammatory cytokines. As shown in figures, co-culture of MC with PMN significantly decreased the production of pro-inflammatory cytokines. The decrease of proinflammatory cytokine secretion by MC was 60- 72% for TNF-α, 52-54% for IL-1β, 46-56% for IL-6 and 66-68% for IL-8. The potential mechanism may occur through soluble receptors inhibiting cytokines such that second phase cytokine production induced by pro-inflammatory cytokines is blocked. The data suggest that neutrophils blunt the levels of proinflammatory cytokines through anti-inflammatory cytokine production to diminish the inflammatory response.FigureTable 1: LPS stimulated Cytokine Secretion (pg)
Strawbies (2015)

In this demo we present Strawbies, a realtime tangible programming game designed for children ages 5 to 10. Strawbies is played by constructing physical programs out of wooden tiles in front of an iPad. This interaction is made possible with the use of an Osmo play system that includes a mirror to reflect images in front of the iPad through the front-facing camera. We combined this system with the TopCodes computer vision library for fast and reliable image recognition. Here we describe a set of principles that guided our iterative design process along with an overview of testing sessions with children that informed our most recent instantiation of Strawbies.
Smart Core−Shell Nanostructure with a Mesoporous Core and a Stimuli-Responsive Nanoshell Synthesized via Surface Reversible Addition−Fragmentation Chain Transfer Polymerization (2008)

A facile and versatile method to prepare mesoporous core−shell nanostructure with a stimuli-responsive nanoshell was reported. Reversible addition−fragmentation chain transfer (RAFT) functionalities were anchored to the mesoporous silica nanoparticle (MSN), and RAFT polymerization of N-isopropylacrylamide (NIPAAm) was subsequently conducted to graft thermo-sensitive PNIPAAm to the exterior surface of the MSN. The nanoshell undergoes reversible switches between solvated, incompact nanoshell and compact nanoshell upon changing the temperature of the solution, which makes this novel core−shell nanostructure highly attractive for controlled release of drugs, DNAs, and proteins.
Modified Cole–Cole plot based on viscoelastic properties for characterizing molecular architecture of elastomers (1984)

Abstract The types of molecular architecture commonly present in many commercial elastomers include long branching, which in extreme cases results in crosslinked gel network. This architecture was modeled by preparing a series of ethylene–propylene copolymer samples in which the degree of branching was systematically varied. The frequency‐dependent viscoelastic properties of these model systems were measured over a temperature range of 80–230°C with a Rheometrics Mechanical Spectrometer. Time–temperature superposition was employed to obtain master curves of the storage G ′ and loss G ″ moduli and complex viscosity. The viscoelastic properties of the model samples change systematically with the variations in molecular architecture. Specifically, the low frequency Newtonian viscosity behavior is progressively replaced by non‐Newtonian power‐law behavior, and the G ′ response relative to that of the G ″ is significantly enhanced as long‐branching increases. The practical use of a modified Cole–Cole plot, in which the axes are expressed as the logarithms of G ′ and G ″, for analysis of molecular architecture is demonstrated. Changes in the long‐branch architecture of the model samples were readily detected as systematic variations in shape and displacement of the modified Cole–Cole plot. On the other hand, the data of molecularly linear elastomer samples of different M w but similar MWDs were reduced to a single master Cole–Cole plot.
Surfactant protein-D and pulmonary host defense (2000)

Surfactant protein-D (SP-D) participates in the innate response to inhaled microorganisms and organic antigens, and contributes to immune and inflammatory regulation within the lung. SP-D is synthesized and secreted by alveolar and bronchiolar epithelial cells, but is also expressed by epithelial cells lining various exocrine ducts and the mucosa of the gastrointestinal and genitourinary tracts. SP-D, a collagenous calcium-dependent lectin (or collectin), binds to surface glycoconjugates expressed by a wide variety of microorganisms, and to oligosaccharides associated with the surface of various complex organic antigens. SP-D also specifically interacts with glycoconjugates and other molecules expressed on the surface of macrophages, neutrophils, and lymphocytes. In addition, SP-D binds to specific surfactant-associated lipids and can influence the organization of lipid mixtures containing phosphatidylinositol in vitro. Consistent with these diverse in vitro activities is the observation that SP-D-deficient transgenic mice show abnormal accumulations of surfactant lipids, and respond abnormally to challenge with respiratory viruses and bacterial lipopolysaccharides. The phenotype of macrophages isolated from the lungs of SP-D-deficient mice is altered, and there is circumstantial evidence that abnormal oxidant metabolism and/or increased metalloproteinase expression contributes to the development of emphysema. The expression of SP-D is increased in response to many forms of lung injury, and deficient accumulation of appropriately oligomerized SP-D might contribute to the pathogenesis of a variety of human lung diseases.
N-terminal sequences from <i>Autographa californica</i> nuclear polyhedrosis virus envelope proteins ODV-E66 and ODV-E25 are sufficient to direct reporter proteins to the nuclear envelope, intranuclear microvesicles and the envelope of occlusion derived virus (1997)

Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. N-terminal amino acid sequences of the Autographa californica nuclear polyhedrosis virus (AcMNPV) envelope proteins, ODV-E66 and ODV-E25 (23 and 24 amino acids, respectively) are highly hydrophobic. Recombinant viruses that express the two N-terminal amino acid sequences fused to green fluorescent protein (23GFP or 24GFP) provided visual markers to follow protein transport and localization within the nucleus during infection. Autoflourescence was first detected along the cytoplasmic periphery of the nucleus and subsequently localized as foci to discrete locations within the nucleus. Immunoelectron microscopy confirmed that these foci predominantly contained intranuclear microvesicles and the reporter fusion proteins were also detected in cytoplasmic membranes near the nucleus, and the outer and inner nuclear membrane. Therefore, these defined hydrophobic domains are sufficient to direct native and fusion proteins to induced membrane microvesicles within a baculovirus-infected cell nucleus and the viral envelope. In addition, these data suggest that movement of these proteins into the nuclear envelope may initiate through cytoplasmic membranes, such as endoplasmic reticulum, and that transport into the nucleus may be mediated through the outer and inner nuclear membrane.
Reflections on a candidate design of the user-interface for a wireless vital-signs monitor (2000)

In this paper we present a case study of our candidate design for the user-interface of a wireless vital-signs monitor. We reflect on our design of the user-interface, and relate our design experience to theories of artefact design, evaluating from this case study how the theories apply to the broader design context of design for AR. Theories of `good design' in artefact design literature do not unilaterally apply to the design for an augmented reality device. In many cases, design in AR fields requires the designer to create new cultural conventions by virtue of the fact that the designer is immersing the user in an unfamiliar environment. Thus, the designer is often unable to utilise affordances and existing cultural conventions because the functions and/or use of the object expands the environment in which affordances and cultural conventions currently have meaning.
Three extensions to subtractive crosstalk reduction (2007)

Stereo displays suffer from crosstalk, an effect that reduces or even inhibits the viewer's ability to correctly fuse stereoscopic images. In this paper, three extensions for improved software crosstalk reduction are introduced. First, we propose a reduction method operating in CIELAB color space to find a perceptually better color match for crosstalk corrected pixels. Second, we introduce a geometry-based reduction method that operates on fused 3D pixels. Finally, a run-time optimization is introduced that avoids the need to process each pixel. We evaluated our CIELAB-based method using the Visible Differences Predictor (VDP). Our results show that we are able to significantly improve crosstalk reduction compared to previously used methods that operate in RGB color space. The combination of our methods provides an improved, real-time software crosstalk reduction framework, applicable to a wider range of scenes, delivering better quality, higher performance, and more flexibility.
Space time coded cooperative relaying technique for multihop communications (2005)

In multihop wireless networks, the quality of communications is degraded due to the relay transmissions over fading channels. Space-time code using multiple transmit antennas is an effective countermeasure for fading. For terminals which have only one antenna due to size/cost limitations, user cooperation has been introduced as a diversity technique. A new cooperative relaying scheme is proposed in order to combat the effects of fading in multihop communications among single antenna terminals. This scheme utilizes space-time code for cooperative relaying and is developed in both frequency-flat and frequency-selective fading channels for exploiting space and path diversity gain. By computer simulations, it is shown that the scheme can achieve almost full spatial diversity in multihop communications by both non-regenerative relaying with SNR estimation and regenerative relaying with error detection.
Phosphorylation of Tau by Cyclic-AMP-Dependent Protein Kinase (1993)

Alzheimer's disease paired helical filaments contain abnormally phosphorylated tau (PHF-tau) which has reduced electrophoretic mobility on sodium dodecyl sulphate polyacrylamide electrophoresis. We have investigated the effects of cyclic-AMP-dependent protein kinase (PKA) on recombinant human tau isoforms and two recombinant tau fragments. PKA phosphorylated tau and reduced its electrophoretic mobility, phosphorylation towards the C-terminus of tau having a major influence on this property. Substitution of serine396 (phosphorylated in PHF-tau) or serine416 (phosphorylated by calcium/calmodulin kinase II) by alanine demonstrated that these are not major sites for PKA phosphorylation. Although the phosphorylated forms of tau generated by PKA are not identical to those of PHF-tau, PKA may be involved in the generation of PHF-tau in Alzheimer's disease via phosphorylation of additional, as yet unidentified, sites on tau.
Three-Dimensional Projection With Circular Polarizers (1984)

Linearly polarized light has been used extensively as a means of encoding and decoding projected, superimposed stereoscopic images. An inherent property of such linear polarizer systems is that the observer wearing 3-D viewers must keep his head erect in order to maintain proper polarizer orientation and avoid troublesome ghost images. Circularly polarized light provides efficient extinction over a wide range of angular rotation, thus providing the opportunity to view 3-D comfortably with great freedom of head motion and position.
The pro α2(V) collagen gene is evolutionarily related to the major fibrillar-forming collagens (1987)

A number of overlapping cDNA clones, covering 5.2 kb of sequences which code for the human pro alpha 2(V) collagen chain, have been isolated. Analysis of the structural data have indicated a close evolutionary kinship between the pro alpha 2(V) chain and the major fibrillar collagen types. Isolation and analysis of an 8 kb genomic fragment has further supported this notion by revealing a homologous arrangement of nine triple-helical domain exons. These studies have therefore provided conclusive evidence which categorizes the Type V collagen as a member of the Group 1 molecules, or fibrillar-forming collagens.
Naphthalene and Anthracene Cobaltates(1−): Useful Storable Sources of an Atomic Cobalt Anion (2012)

Reductions of CoBr(2) or cobaltocene by 3 equiv of potassium anthracene radical anion in tetrahydrofuran (THF) afford 60-80% yields of bis(anthracene)cobaltate(1-) (1), of interest as a readily accessible and quite labile source of spin-paired atomic Co(-). Although the unsolvated potassium salt of 1 is thermally unstable at 20 °C, the [K(18-crown-6)(THF)(2)](+) salt of 1 functions as a useful storable crystalline reagent for Co(-) in several reactions. Previously known classic cobaltates, [CoL(4)](-), for L = 1/2 (1,3-butadiene) (2), PF(3) (3), and P(OiPr)(3) (5), were obtained directly from 1 and structurally characterized for the first time. Anion 3 is noteworthy because it appears to possess the shortest known Co-P distance, av = 2.012(4) Å. Although the naphthalene analogue of 1 is not yet available as a pure substance, low-temperature reductions of CoBr(2) or cobaltocene by naphthalene radical anion in the presence of 1,5-cyclooctadiene (COD) afford variable yields (80-90% from CoCp(2)) of (naphthalene)(COD)cobaltate(1-) (10). Ready displacement of naphthalene in 10 by L = 1,3-butadiene, 2,2'-bipyridine, and COD occurs to give good yields of the respective [Co(L)(COD)](-), all of which have been structurally characterized. Both ligands in 10 are displaced by tert-butylisocyanide to afford [Co(CNtBu)(4)](-) (16), the first isolable and structurally characterized homoleptic alkylisocyanometalate. The molecular structure of 16 shows unprecedented bending of the isocyanides, av C-N-C = 137(2)°, for homoleptic isocyanide complexes.
Direct Observation of Boundary Layers (1996)

By using a combination of spacer layer optical interferometry and spectral analysis, it has recently become possible to measure lubricant films down to less than 2 nm thickness in high-pressure, rolling ball on flat contacts. This enables the presence and some of the properties of boundary lubricating films to be observed directly for the first time in realistic contact conditions. This paper describes some recent work using this approach. It is shown that highly refined, nonpolar base fluids exhibit classical hydrodynamic behavior down to less than 2 nm film thickness, whereas fluids such as esters give enhanced film thickness in this very thin film region. Work on polymer solutions and base fluid mixtures suggests that the main way that such fluids form boundary layers is by preferential adsorption on solid surfaces of polar moieties from solution. This has the effect of changing the composition and thus effective viscosity of lubricant layers close to solid surfaces, thereby leading to a hydrodynamic response different from that predicted from the bulk rheological properties of the blend.
Facile Synthesis of [6,6]-Phenyl-C61/71-Butyric Acid Methyl Esters via Sulfur Ylides for Bulk-Heterojunction Solar Cell (2013)

A one-step, mild synthesis of methanofullerenes as electron acceptors for solution-processed bulk-heterojunction solar cells was developed. [6,6]-Phenyl-C<sub>61</sub>-butyric acid methyl ester {[60]PCBM} was directly synthesized in good yields, by the reaction of fullerene with sulfur ylide derivatives in the presence of 1,8-diazabicyclo-[5.4.0]undec-7-ene (DBU) at room temperature. This method was also successfully applied to the preparation of [6,6]-phenyl-C<sub>71</sub>-butyric acid methyl ester {[70]PCBM}.
Genetic approach to feature selection for ensemble creation (1999)

Ensembles of classifiers have been shown to be very effective for case-based classification tasks. The vast majority of ensemble construction algorithms use the complete set of features available in the problem domain for the ensemble creation. Recent work on randomly selected subspaces for ensemble construction has been shown to improve the accuracy of the ensemble considerably. In this paper we focus our attention on feature selection for ensemble creation using a genetic search approach. We compare boosting and bagging techniques using three approaches for feature selection for ensemble construction.
Role of the H Protein in Assembly of the Photochemical Reaction Center and Intracytoplasmic Membrane in <i>Rhodospirillum rubrum</i> (2000)

Rhodospirillum rubrum is a model for the study of membrane formation. Under conditions of oxygen limitation, this facultatively phototrophic bacterium forms an intracytoplasmic membrane that houses the photochemical apparatus. This apparatus consists of two pigment-protein complexes, the light-harvesting antenna (LH) and photochemical reaction center (RC). The proteins of the photochemical components are encoded by the puf operon (LHalpha, LHbeta, RC-L, and RC-M) and by puhA (RC-H). R. rubrum puf interposon mutants do not form intracytoplasmic membranes and are phototrophically incompetent. The puh region was cloned, and DNA sequence determination identified open reading frames bchL and bchM and part of bchH; bchHLM encode enzymes of bacteriochlorophyll biosynthesis. A puhA/G115 interposon mutant was constructed and found to be incapable of phototrophic growth and impaired in intracytoplasmic membrane formation. Comparison of properties of the wild-type and the mutated and complemented strains suggests a model for membrane protein assembly. This model proposes that RC-H is required as a foundation protein for assembly of the RC and highly developed intracytoplasmic membrane. In complemented strains, expression of puh occurred under semiaerobic conditions, thus providing the basis for the development of an expression vector. The puhA gene alone was sufficient to restore phototrophic growth provided that recombination occurred.
Quantal phase factors accompanying adiabatic changes (1984)

Abstract A quantal system in an eigenstate, slowly transported round a circuit C by varying parameters R in its Hamiltonian Ĥ(R), will acquire a geometrical phase factor exp{iγ(C)} in addition to the familiar dynamical phase factor. An explicit general formula for γ(C) is derived in terms of the spectrum and eigenstates of Ĥ(R) over a surface spanning C. If C lies near a degeneracy of Ĥ, γ(C) takes a simple form which includes as a special case the sign change of eigenfunctions of real symmetric matrices round a degeneracy. As an illustration γ(C) is calculated for spinning particles in slowly-changing magnetic fields; although the sign reversal of spinors on rotation is a special case, the effect is predicted to occur for bosons as well as fermions, and a method for observing it is proposed. It is shown that the Aharonov-Bohm effect can be interpreted as a geometrical phase factor.