gebhart/patrepeval huggingface dataset:
Environment-assisted quantum walks in photosynthetic energy transfer (2008)

Energy transfer within photosynthetic systems can display quantum effects such as delocalized excitonic transport. Recently, direct evidence of long-lived coherence has been experimentally demonstrated for the dynamics of the Fenna-Matthews-Olson (FMO) protein complex [Engel et al., Nature (London) 446, 782 (2007)]. However, the relevance of quantum dynamical processes to the exciton transfer efficiency is to a large extent unknown. Here, we develop a theoretical framework for studying the role of quantum interference effects in energy transfer dynamics of molecular arrays interacting with a thermal bath within the Lindblad formalism. To this end, we generalize continuous-time quantum walks to nonunitary and temperature-dependent dynamics in Liouville space derived from a microscopic Hamiltonian. Different physical effects of coherence and decoherence processes are explored via a universal measure for the energy transfer efficiency and its susceptibility. In particular, we demonstrate that for the FMO complex, an effective interplay between the free Hamiltonian evolution and the thermal fluctuations in the environment leads to a substantial increase in energy transfer efficiency from about 70% to 99%.
Suspended core subwavelength fibers: towards practical designs for low-loss terahertz guidance (2011)

In this work we report two designs of subwavelength fibers packaged for practical terahertz wave guiding. We describe fabrication, modeling and characterization of microstructured polymer fibers featuring a subwavelength-size core suspended in the middle of a large porous outer cladding. This design allows convenient handling of the subwavelength fibers without distorting their modal profile. Additionally, the air-tight porous cladding serves as a natural enclosure for the fiber core, thus avoiding the need for a bulky external enclosure for humidity-purged atmosphere. Fibers of 5 mm and 3 mm in outer diameters with a 150 µm suspended solid core and a 900 µm suspended porous core respectively, were obtained by utilizing a combination of drilling and stacking techniques. Characterization of the fiber optical properties and the subwavelength imaging of the guided modes were performed using a terahertz near-field microscopy setup. Near-field imaging of the modal profiles at the fiber output confirmed the effectively single-mode behavior of such waveguides. The suspended core fibers exhibit transmission from 0.10 THz to 0.27 THz (larger core), and from 0.25 THz to 0.51 THz (smaller core). Due to the large fraction of power that is guided in the holey cladding, fiber propagation losses as low as 0.02 cm(-1) are demonstrated specifically for the small core fiber. Low-loss guidance combined with the core isolated from environmental perturbations make these all-dielectric fibers suitable for practical terahertz imaging and sensing applications.
Evaluating the Impact of Intravitreal Aflibercept on Diabetic Retinopathy Progression in the VIVID-DME and VISTA-DME Studies (2018)

These analyses demonstrate the benefit of intravitreal aflibercept over laser with respect to DR progression, suggesting a benefit on DME, and on underlying DR.
Retrogenic Modeling of Experimental Allergic Encephalomyelitis Associates T Cell Frequency but Not TCR Functional Affinity with Pathogenicity (2008)

The properties of a self-specific T cell's TCR that determine its pathogenicity are not well understood. We developed TCR retroviral transgenic, or retrogenic, models of myelin oligodendroglial glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE) to compare the pathologic potential of five H-2 Ab/MOG35-55-specific TCRs. The TCRs were cloned and retrovirally transduced into either TCRalphabeta-deficient hybridoma cells or Rag1-/- bone marrow progenitor cells. Comparison of the hybridomas, identical except for TCR sequence, revealed distinct responsiveness, or functionally determined affinity, for cognate Ag. Retrogenic mice were produced by transfer of transduced progenitor cells into Rag1-/- recipients. T cells were detected within 4 wk. Engraftment levels varied considerably among the different TCRs and showed separate variability among individual mice. T cells were predominantly naive and virtually exclusively CD4+ and CD25-. Relative responses of the retrogenic T cells to Ag paralleled those of the hybridoma cells. Induction of EAE through active immunization led to rapid and severe disease in all mice expressing MOG-specific TCR. The mice additionally developed spontaneous disease, the incidence of which varied with the individual receptors. Interestingly, spontaneous disease frequency and intensity could not be correlated with the functional affinity of the respective TCR. Instead, it was associated with engraftment level, even when measured weeks before the onset of disease symptoms. Our results demonstrate the feasibility of using retrogenic modeling to compare TCRs in the EAE system. They further suggest that affinity is not a primary determinant in spontaneous EAE development in mice expressing monotypic TCRs and that autoreactive T cell frequency is of greater significance.
CD33 Detection by Immunohistochemistry in Paraffin-Embedded Tissues (2008)

A new monoclonal antibody to CD33 that reacts in paraffin-embedded tissue samples was evaluated. The expected reactivity in granulocytic and monocytic cells was found in a tissue microarray composed of multiple tissue sites. There was no unexpected reactivity found in a wide variety of hematolymphoid and nonhematolymphoid disorders. In cases of acute leukemia, the CD33 antibody showed equivalent results by immunohistochemical analysis compared with flow cytometric analysis. The CD33 antibody was also found to be a useful marker in the workup of myeloid sarcomas. This anti-CD33 antibody will be a useful marker in the workup of acute leukemias and myeloid sarcomas on paraffin-embedded tissue samples.
N-terminal stretch Arg2, Arg3, Arg4 and Arg5 of human lactoferrin is essential for binding to heparin, bacterial lipopolysaccharide, human lysozyme and DNA (1997)

Human lactoferrin (hLF), a protein involved in host defence against infection and excessive inflammation, interacts with heparin, the lipid A moiety of bacterial lipopolysaccharide, human lysozyme (hLZ) and DNA. To determine which region of the molecule is important in these interactions, solid-phase ligand binding assays were performed with hLF from human milk (natural hLF) and N-terminally deleted hLF variants. Iron-saturated and natural hLF bound equally well to heparin, lipid A, hLZ and DNA. Natural hLF lacking the first two N-terminal amino acids (Gly1-Arg2) showed reactivities of one-half, two-thirds, one-third and one-third towards heparin, lipid A, hLZ and DNA respectively compared with N-terminally intact hLF. A lack of the first three residues (Gly1-Arg2-Arg3) decreased binding to the same ligands to one-eighth, one-quarter, one-twentieth and one-seventeenth respectively. No binding occurred with a mutant lacking the first five residues (Gly1-Arg2-Arg3-Arg4-Arg5). An anti-hLF monoclonal antibody (E11) that reacts to an N-lobe epitope including Arg5 completely blocked hLF-ligand interaction. These results show that the N-terminal stretch of four consecutive arginine residues, Arg2-Arg3-Arg4-Arg5, has a decisive role in the interaction of hLF with heparin, lipid A, hLZ and DNA. The role of limited N-terminal proteolysis of hLF in its anti-infective and anti-inflammatory properties is discussed.
Scale-invariant range features for time-of-flight camera applications (2008)

We describe a technique for computing scale-invariant features on range maps produced by a range sensor, such as a time-of-flight camera. Scale invariance is achieved by computing the features on the reconstructed three-dimensional surface of the object. The technique is general and can be applied to a wide range of operators. Features are computed in the frequency domain; the transform from the irregularly sampled mesh to the frequency domain uses the Nonequispaced Fast Fourier Transform. We demonstrate the technique on a facial feature detection task. On a dataset containing faces at various distances from the camera, the equal error rate (EER) for the case of scale-invariant features is halved compared to features computed on the range map in the conventional way. When the scale-invariant range features are combined with intensity features, the error rate on the test set reduces to zero.
Retinoic Acid-induced Gene-1 (RIG-I) Associates with the Actin Cytoskeleton via Caspase Activation and Recruitment Domain-dependent Interactions (2009)

The actin cytoskeleton serves as a barrier that protects mammalian cells from environmental pathogens such as bacteria, fungi, and viruses. Several components of antimicrobial signaling pathways have been shown to associate directly with the actin cytoskeleton, indicating that the cytoskeleton may also serve as a platform for immune-associated molecules. Here we report that retinoic acid-induced gene-I (RIG-I), an important viral RNA recognition molecule, is associated with the actin cytoskeleton and localizes predominantly to actin-enriched membrane ruffles in non-polarized epithelial cells. Subcellular localization and fractionation experiments revealed that the association between RIG-I and the actin cytoskeleton was mediated by its N-terminal caspase activation and recruitment domains (CARDs), which were necessary and sufficient to induce cytoskeletal association. We also show that RIG-I plays a role in cellular migration, as ectopic expression of RIG-I enhanced cellular migration in a wound healing assay and depletion of endogenous RIG-I significantly reduced wound healing. We further show that in both cultured intestinal epithelial cells (IEC) and human colon and small intestine biopsies, RIG-I is enriched at apico-lateral cell junctions and colocalizes with markers of the tight junction. Depolymerization of the actin cytoskeleton in polarized IEC led to the rapid relocalization of RIG-I and to the induction of type I interferon signaling. These data provide evidence that RIG-I is associated with the actin cytoskeleton in non-polarized epithelial cells and with the junctional complex in polarized IECs and human intestine and colon biopsies and may point to a physiological role for RIG-I in the regulation of cellular migration.
A Morphological Model for the Solvent‐Enhanced Conductivity of PEDOT:PSS Thin Films (2008)

Abstract The well‐known enhanced conductivity of poly(3,4‐ethylenedioxythiophene):poly(4‐styrenesulfonate) (PEDOT:PSS) thin films that is obtained by addition of high‐boiling solvents like sorbitol to the aqueous dispersion used for film deposition is shown to be associated with a rearrangement of PEDOT‐rich clusters into elongated domains, as evidenced from STM and AFM. Consistently, temperature dependent conductivity measurements for sorbitol‐treated films reveal that charge transport occurs via quasi 1D variable range hopping (VRH), in contrast to 3D VRH for untreated PEDOT:PSS films. The typical hopping distance of 60–90 nm, extracted from the conductivity measurements is consistent with hopping between the 30–40 nm sized grains observed with scanning probe microscopy.
Money, glory and cheap talk (2010)

Crowdsourcing is a new Web phenomenon, in which a firm takes a function once performed in-house and outsources it to a crowd, usually in the form of an open contest.Designing efficient crowdsourcing mechanisms is not possible without deep understanding of incentives and strategic choices of all participants.This paper presents an empirical analysis of determinants of individual performance in multiple simultaneous crowdsourcing contests using a unique dataset for the world's largest competitive software development portal: TopCoder.com. Special attention is given to studying the effects of the reputation system currently used by TopCoder.com on behavior of contestants. We find that individual specific traits together with the project payment and the number of project requirements are significant predictors of the final project quality. Furthermore, we find significant evidence of strategic behavior of contestants. High rated contestants face tougher competition from their opponents in the competition phase of the contest. In order to soften the competition, they move first in the registration phase of the contest, signing up early for particular projects. Although registration in TopCoder contests is non-binding, it deters entry of opponents in the same contest; our lower bound estimate shows that this strategy generates significant surplus gain to high rated contestants. We conjecture that the reputation + cheap talk mechanism employed by TopCoder has a positive effect on allocative efficiency of simultaneous all-pay contests and should be considered for adoption in other crowdsourcing platforms.
Modification of Medical Device Surface to Attain Anti-Infection (2004)

Extensive use of antibiotics to treat device-associated infections has contributed to the acceleration of the appearance of antibiotic-resistant bacteria by spreading through contaminated hospital environments to patients (1,2). Comprehensive research has had limited success in the reduction of device-associated infections, and usually the only therapy to treat the infections is removal of the infected devices from patients. Recent strategies to minimize the risks of device-associated infections have focused on the following areas: good clinical practices, prudent selection of biomaterials used for device construction, and modification of device surfaces by increasing surface biocompatibility and decreasing bacterial adherence. The elements of bacterial adhesion on indwelling device surfaces that may directly relate to infections and will study surface treatment technologies in reducing the incidence of indwelling medical device-related infections. In the following text these topics will be discussed from several aspects.
Development of oral osteomucosal tissue constructs in vitro and localization of fluorescently-labeled bisphosphonates to hard and soft tissue (2014)

Bisphosphonates (BPs) are anti-resorptive agents commonly used to treat bone-related diseases; however, soft tissue-related side-effects are frequently reported in some BP users, such as oral or gastrointestinal (GI) ulcerations. BPs are stable analogs of pyrophosphate and have high affinity to hydroxyapatite, allowing them to bind to the bone surfaces and exert suppressive effects on osteoclast functions. However, the underlying mechanisms as to how bone-seeking BPs also exert cytotoxic effects on soft tissue remain unknown. In the present study, we investigated the localization of nitrogen-containing BPs (N-BPs) in hard and soft tissue using fluorescently-labeled N-BPs in vitro. We developed osteomucosal tissue constructs in vitro to recapitulate the hard and soft tissue of the oral cavity. A histological examination of the osteomucosal tissue constructs revealed a differentiated epithelium over the bone containing osteocytes and the periosteum, similar to that observed in the rat palatal tissues. Following treatment with the fluorescently-labeled bisphosphonate, AF647-ZOL, the osteomucosal constructs exhibited fluorescent signals, not only in the bone, but also in the epithelium. No fluorescent signals were observed from the control- or ZOL-treated constructs, as expected. Collectively, the data from the present study suggest that N-BPs localize to epithelial tissue and that such a localization and subsequent toxicity of N-BPs may be associated, at least in part, with soft tissue-related side-effects.
STM Control of Chemical Reactions: Single-Molecule Synthesis (2003)

The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.
Crucial roles of Foxa2 in mouse anterior–posterior axis polarization via regulation of anterior visceral endoderm-specific genes (2007)

Anterior visceral endoderm (AVE) plays essential roles with respect to anterior-posterior axis development in the early mouse embryo. To assess the genetic cascade involved in AVE formation, the cis-regulatory elements directing expression of vertebrate Otx2 genes in the AVE were analyzed via generation of transgenic mice. Otx2 expression in AVE is regulated directly by the forkhead transcription factor, Foxa2. Moreover, Foxa2 is essential for expression of the Wnt antagonists, Dkk1 and Cerl, in visceral endoderm during the pre- to early streak stages; however, Foxa2 appears to be dispensable for subsequent Dkk1 expression associated with forebrain induction. Thus, we propose that Foxa2 is crucial in early anterior-posterior axis polarization in terms of regulation of expression of AVE-specific genes. These findings provide profound insights into conserved roles of Foxa2 transcription factors in anterior specification throughout the evolution of the chordate body plan.
Pregnancy-associated Plasma Protein-A2 (PAPP-A2), a Novel Insulin-like Growth Factor-binding Protein-5 Proteinase (2001)

A novel metalloproteinase with similarity to pregnancy-associated plasma protein-A (PAPP-A), which we denoted PAPP-A2, has been identified. Through expression in mammalian cells we showed that recombinant PAPP-A2 polypeptide of 1558 residues resulted from processing of a 1791-residue prepro-protein. Unlike PAPP-A, PAPP-A2 migrated as a monomer (of 220 kDa) in non-reducing SDS-polyacrylamide gel electrophoresis. The prepro-parts of PAPP-A2 and PAPP-A are not homologous, but mature PAPP-A2 shares 45% of its residues with PAPP-A. Because PAPP-A specifically cleaves insulin-like growth factor-binding protein (IGFBP)-4, one of six known modulators of IGF-I and -II, we looked for a possible PAPP-A2 substrate among the members of this family. We showed that PAPP-A2 specifically cleaved IGFBP-5 at one site, between Ser-143 and Lys-144. In contrast to the cleavage of IGFBP-4 by PAPP-A that strictly requires the presence of IGF, the cleavage of IGFBP-5 by PAPP-A2 was IGF-independent. Recent data firmly establish PAPP-A and IGFBP-4 as an important functional pair in several systems. Because of its close relationship with PAPP-A, both structurally and functionally, PAPP-A2 is a likely candidate IGFBP-5 proteinase in many tissues and conditioned media where IGFBP-5 proteolysis has been reported.
Muc2 Protects against Lethal Infectious Colitis by Disassociating Pathogenic and Commensal Bacteria from the Colonic Mucosa (2010)

Despite recent advances in our understanding of the pathogenesis of attaching and effacing (A/E) Escherichia coli infections, the mechanisms by which the host defends against these microbes are unclear. The goal of this study was to determine the role of goblet cell-derived Muc2, the major intestinal secretory mucin and primary component of the mucus layer, in host protection against A/E pathogens. To assess the role of Muc2 during A/E bacterial infections, we inoculated Muc2 deficient (Muc2(-/-)) mice with Citrobacter rodentium, a murine A/E pathogen related to diarrheagenic A/E E. coli. Unlike wildtype (WT) mice, infected Muc2(-/-) mice exhibited rapid weight loss and suffered up to 90% mortality. Stool plating demonstrated 10-100 fold greater C. rodentium burdens in Muc2(-/-) vs. WT mice, most of which were found to be loosely adherent to the colonic mucosa. Histology of Muc2(-/-) mice revealed ulceration in the colon amid focal bacterial microcolonies. Metabolic labeling of secreted mucins in the large intestine demonstrated that mucin secretion was markedly increased in WT mice during infection compared to uninfected controls, suggesting that the host uses increased mucin release to flush pathogens from the mucosal surface. Muc2 also impacted host-commensal interactions during infection, as FISH analysis revealed C. rodentium microcolonies contained numerous commensal microbes, which was not observed in WT mice. Orally administered FITC-Dextran and FISH staining showed significantly worsened intestinal barrier disruption in Muc2(-/-) vs. WT mice, with overt pathogen and commensal translocation into the Muc2(-/-) colonic mucosa. Interestingly, commensal depletion enhanced C. rodentium colonization of Muc2(-/-) mice, although colonic pathology was not significantly altered. In conclusion, Muc2 production is critical for host protection during A/E bacterial infections, by limiting overall pathogen and commensal numbers associated with the colonic mucosal surface. Such actions limit tissue damage and translocation of pathogenic and commensal bacteria across the epithelium.
Dextran magnetite as a liver contrast agent (1991)

The superparamagnetic particle dextran magnetite was studied as a liver tumor contrast agent for magnetic resonance imaging (MRI). The effects of dextran magnetite on the longitudinal (T1) and transverse (T2) relaxation times in liver, spleen, and an implanted rat liver tumor were measured at 0.47 T (IBM/Bruker PC-20 relaxometer) over the dose range of 23 to 69 mumol Fe/kg. Dextran magnetite substantially reduced the T2 of the liver and spleen, but not of the tumor, thereby providing a basis for improved tumor imaging. The T1 of the tumor was not affected following injection of dextran magnetite in the dose range studied, while the spleen T1 was reduced substantially more than the T1 of the liver. Histological studies using the iron reaction for Prussian blue clearly showed dextran magnetite in the liver and spleen, but not in the tumor. While dextran magnetite was sequestered in macrophages in both liver and spleen, the distribution in the liver was more diffuse (70 microns average particle separation) than that in the spleen (25 microns separation). The lack of a T1 effect in the liver is consistent with the fact that a majority of the water in the tissue cannot diffuse to the relaxational centers on the time scale of the liver's intrinsic T1 (280 ms). In the spleen, however, the dextran magnetite is more densely packed in the red pulp allowing a significant fraction of the water to be relaxed by a T1 mechanism. Spin-echo images of the implanted tumor (mammary adenocarcinoma. R3230AC) in the livers of Fischer 344 rats were obtained at 0.50 T (Siemens Magnetom). The tumor-to-liver contrast was improved for both T1 and T2-weighted spin-echo images after intravenous injection of the dextran magnetite contrast agent. The contrast determined from these images agreed with that predicted by the measured T1 and the T2 (Hahn spin-echo) values. In addition, gradient-echo T2-weighted images with good contrast were obtained in a much shorter imaging time than was needed for T2-weighted spin-echo images. These results demonstrate that the MRI contrast enhancement observed with dextran magnetite is based on its selective uptake and distribution in the macrophages in the liver and spleen and that this agent has substantial potential as a superparamagnetic MR contrast agent.