Enhancement of Magnetic Stability in Antiferromagnetic CoO Films by Adsorption of Organic Molecules.

Antiferromagnets are a class of magnetic materials of great interest in spintronic devices because of their stability and ultrafast dynamics. When interfaced with an organic molecular layer, antiferromagnetic (AF) films are expected to form a spinterface that can allow fine control of specific AF properties. In this paper, we investigate spinterface effects on CoO, an AF oxide. To access the magnetic state of the antiferromagnet, we couple it to a ferromagnetic Co film via an exchange bias (EB) effect. In this way, the formation of a spinterface is detected through changes induced on the CoO/Co EB system. We demonstrate that C60 and Gaq3 adsorption on CoO shifts its blocking temperature; in turn, an increase in both the EB fields and the coercivities is observed on the EB-coupled Co layer. Ab initio calculations for the CoO/C60 interface indicate that the molecular adsorption is responsible for a charge redistribution on the CoO layer that alters the occupation of the d orbitals of Co atoms and, to a smaller extent, the p orbitals of oxygen. As a result, the AF coupling between Co atoms in the CoO is enhanced. Considering the granular nature of CoO, a larger AF stability upon molecular adsorption is then associated with a larger number of AF grains that are stable upon reversal of the Co layer.

Surface Roughness-Induced Changes in Important Physical Features of CoFeSm Thin Films on Glass Substrates during Annealing.

Co60Fe20Sm20 thin films were deposited onto glass substrates in a high vacuum setting. The films varied in thickness from 10 to 50 nm and underwent annealing processes at different temperatures: room temperature (RT), 100, 200, and 300 °C. Our analysis encompassed structural, magnetic, electrical, nanomechanical, adhesive, and optical properties in relation to film thickness and annealing temperature. X-ray diffraction (XRD) analysis did not reveal characteristic peaks in Co60Fe20Sm20 thin films due to insufficient growth-driving forces. Electrical measurements indicated reduced resistivity and sheet resistance with increasing film thickness and higher annealing temperatures, owing to hindered current-carrier transport resulting from the amorphous structure. Atomic force microscope (AFM) analysis showed a decrease in surface roughness with increased thickness and annealing temperature. The low-frequency alternating current magnetic susceptibility (χac) values increased with film thickness and annealing temperature. Nanoindentation analysis demonstrated reduced film hardness and Young's modulus with thicker films. Contact angle measurements suggested a hydrophilic film. Surface energy increased with greater film thickness, particularly in annealed films, indicating a decrease in contact angle contributing to this increase. Transmittance measurements have revealed intensified absorption and reduced transmittance with thicker films. In summary, the surface roughness of CoFeSm films at different annealing temperatures significantly influenced their magnetic, electrical, adhesive, and optical properties. A smoother surface reduced the pinning effect on the domain walls, enhancing the χac value. Additionally, diminished surface roughness led to a lower contact angle and higher surface energy. Additionally, smoother surfaces exhibited higher carrier conductivity, resulting in reduced electrical resistance. The optical transparency decreased due to the smoother surface of Co60Fe20Sm20 films.

Effect of Annealing and Thickness of Co40Fe40Yb20 Thin Films on Various Physical Properties on a Glass Substrate.

The aim of this work is to investigate the effect of annealing and thickness on various physical properties in Co40Fe40Yb20 thin films. X-ray diffraction (XRD) was used to determine the amorphous structure of Co40Fe40Yb20 films. The maximum surface energy of 40 nm thin films at 300 °C is 34.54 mJ/mm2. The transmittance and resistivity decreased significantly as annealing temperatures and thickness increased. At all conditions, the 10 nm film had the highest hardness. The average hardness decreased as thickness increased, as predicted by the Hall-Petch effect. The highest low-frequency alternative-current magnetic susceptibility (χac) value was discovered when the film was annealed at 200 °C with 50 nm, and the optimal resonance frequency (ƒres) was in the low frequency range, indicating that the film has good applicability in the low frequency range. At annealed 200 °C and 50 nm, the maximum saturation magnetization (Ms) was discovered. Thermal disturbance caused the Ms to decrease when the temperature was raised to 300 °C. The optimum process conditions determined in this study are 200 °C and 50 nm, with the highest Ms, χac, strong adhesion, and low resistivity, which are suitable for magnetic applications, based on magnetic properties and surface energy.

Antibody Watch: Text mining antibody specificity from the literature.

Antibodies are widely used reagents to test for expression of proteins and other antigens. However, they might not always reliably produce results when they do not specifically bind to the target proteins that their providers designed them for, leading to unreliable research results. While many proposals have been developed to deal with the problem of antibody specificity, it is still challenging to cover the millions of antibodies that are available to researchers. In this study, we investigate the feasibility of automatically generating alerts to users of problematic antibodies by extracting statements about antibody specificity reported in the literature. The extracted alerts can be used to construct an "Antibody Watch" knowledge base containing supporting statements of problematic antibodies. We developed a deep neural network system and tested its performance with a corpus of more than two thousand articles that reported uses of antibodies. We divided the problem into two tasks. Given an input article, the first task is to identify snippets about antibody specificity and classify if the snippets report that any antibody exhibits non-specificity, and thus is problematic. The second task is to link each of these snippets to one or more antibodies mentioned in the snippet. The experimental evaluation shows that our system can accurately perform the classification task with 0.925 weighted F1-score, linking with 0.962 accuracy, and 0.914 weighted F1 when combined to complete the joint task. We leveraged Research Resource Identifiers (RRID) to precisely identify antibodies linked to the extracted specificity snippets. The result shows that it is feasible to construct a reliable knowledge base about problematic antibodies by text mining.

Photo-spin-voltaic effect in PtMn/Y3Fe5O12 thin films.

The photo-spin-voltaic effect is revealed by the presence of a spin voltage generated by photons when a non-magnetic metal (e.g., Pt) is in close proximity to a ferrimagnetic insulator (e.g., Y3Fe5O12 (YIG)). This is attributed to the excited electrons and holes diffusing from the proximized layer near the interface to the metallic surface. By using a dual-ion-beam sputtering deposition technique, a metallic PtMn layer was deposited on YIG /Gd3Ga5O12 (GGG) (111) substrates. We report on the photo-induced-spin voltaic effect in a PtMn/YIG/GGG heterostructure. The sign of the photo-generated voltage was found to switch with magnetic field polarity and its intensity to decrease with increasing PtMn thickness. This indicates that spin-polarized electrons are confined near the interface in the metal. Photo-excitation of these carriers, together with spin-orbit coupling with Pt atoms, is at the origin of the measured transverse voltage. The design may find applications in antiferromagnetic spintronics.

Developing a Semantic Model to Describe Physical Activity Data.

The importance of data in the social and behavioral domains to biomedical research is increasing, but ensuring the reusability of such data through standardization is not a trivial task. To start addressing this challenge, we developed a semantic model of the physical activity domain by reviewing 302 physical activity questions collected from standardized questionnaires and public data repositories. Our semantic model is comprised of activity keywords, qualifiers, response measures and context. We identified three types of contexts: active lifestyle, physical capacity, and environment. The majority (94%) of the 204 activity keywords extracted from the 302 questions were mapped to the UMLS Metathesaurus. Preliminary evaluation of our model with 309 additional activity questions showed that the majority of the questions were related to one of the three context categories. We also noted the need to expand context categories to incorporate the questions assessing psychological aspects of dealing with physical activities.

T cells and lung injury. Impact of rapamycin.

Acute lung injury (ALI) is characterized by pulmonary inflammation and edema. Innate immune cells (e.g., neutrophils and macrophages) are major contributors to inflammation in ALI. Less is known regarding the role of T cells. We examined the effects of rapamycin on inflammation in a LPS-induced murine model of ALI. Rapamycin was administered before and after initiation of injury. Inflammatory parameters, including bronchoalveolar lavage cell counts, T cell surface markers (i.e., cytotoxic T lymphocyte antigen 4 [CTLA4] and fork head-winged helix transcription factor [Foxp3]), T cell activation (CD69), IL-6, and IL-10 were analyzed. Rapamycin significantly decreased inflammatory parameters and decreased Foxp3, CTLA4, and CD69 in CD4(+) T cells. Rapamycin administration before or after the onset of lung injury, as well as systemically or by pulmonary routes, ameliorates inflammation in ALI.

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net.

Phenotype Information Retrieval for Existing GWAS Studies.

The database of Genotypes and Phenotypes (dbGaP) is archiving the results of different Genome Wide Association Studies (GWAS). dbGaP has a multitude of phenotype variables, but they are not harmonized across studies. We proposed a method to standardize phenotype variables by classifying similar variables based on semantic distances. We first extracted variables description, enriched them using domain knowledge, and computed the distances among them. We used clustering techniques to classify the most similar variables. We used domain experts to audit clusters, annotated the clusters with appropriate labels, and used re-clustering to build a semantically-driven Genotypes and Phenotypes (sdGaP) ontology using the UMLS semantic network and metathesaurus. The sdGaP ontology allowed us to expand user queries and retrieve information using a semantic metric called density measure (DM). We illustrated the potential improvement of information retrieval using the sdGaP ontology in one search scenario using the variables from the Cleveland Family Study.

Standardizing Phenotype Variables in the Database of Genotypes and phenotypes (dbGaP) based on Information Models.

This paper describes an information model based approach to standardizing phenotype variables in dbGaP. Our attempt to utilize existing information models of Clinical Element Models (CEM) was not successful although CEM provided a robust means of representing clinical data. Thus, we developed information models derived from phenotype variable descriptions and standardized phenotype variables by fitting them into the models using a simple Natural Language Processing (NLP) algorithm. We report the experience of standardizing findings related variables, which tend to be more idiosyncratic thus pose more challenges to standardization, using this approach.

Feasibility of using Clinical Element Models (CEM) to standardize phenotype variables in the database of genotypes and phenotypes (dbGaP).

The database of Genotypes and Phenotypes (dbGaP) contains various types of data generated from genome-wide association studies (GWAS). These data can be used to facilitate novel scientific discoveries and to reduce cost and time for exploratory research. However, idiosyncrasies and inconsistencies in phenotype variable names are a major barrier to reusing these data. We addressed these challenges in standardizing phenotype variables by formalizing their descriptions using Clinical Element Models (CEM). Designed to represent clinical data, CEMs were highly expressive and thus were able to represent a majority (77.5%) of the 215 phenotype variable descriptions. However, their high expressivity also made it difficult to directly apply them to research data such as phenotype variables in dbGaP. Our study suggested that simplification of the template models makes it more straightforward to formally represent the key semantics of phenotype variables.

Text Categorization of Heart, Lung, and Blood Studies in the Database of Genotypes and Phenotypes (dbGaP) Utilizing n-grams and Metadata Features.

The database of Genotypes and Phenotypes (dbGaP) allows researchers to understand phenotypic contribution to genetic conditions, generate new hypotheses, confirm previous study results, and identify control populations. However, effective use of the database is hindered by suboptimal study retrieval. Our objective is to evaluate text classification techniques to improve study retrieval in the context of the dbGaP database. We utilized standard machine learning algorithms (naive Bayes, support vector machines, and the C4.5 decision tree) trained on dbGaP study text and incorporated n-gram features and study metadata to identify heart, lung, and blood studies. We used the χ(2) feature selection algorithm to identify features that contributed most to classification performance and experimented with dbGaP associated PubMed papers as a proxy for topicality. Classifier performance was favorable in comparison to keyword-based search results. It was determined that text categorization is a useful complement to document retrieval techniques in the dbGaP.

Regulation of cytotoxic T lymphocyte antigen 4 by cyclic AMP.

Recent studies indicate that cyclic AMP (cAMP) induces cytotoxic T lymphocyte antigen (CTLA) 4. CTLA4 is expressed in T cells, and is a negative regulator of T cell activation. CTLA4 expression is regulated by T cell receptor plus CD28 (adaptive immune signaling) at both the transcriptional and post-transcriptional level. Here, we examine the pathways by which cAMP regulates CTLA4 expression, focusing on transcriptional activation. Elevating intracellular cAMP levels by cell-permeable cAMP analogs, the adenylyl cyclase activator, forskolin, or phosphodiesterase inhibitors increases CTLA4 mRNA expression in EL4 murine T cells and primary CD4(+) T cells. Activation of protein kinase A (using the protein kinase A-selective agonist, N6-phenyladenosine-cAMP), but not exchange proteins activated by cAMP (using the exchange proteins activated by cAMP-selective 8-pCPT-2Me-cAMP), increases CTLA4 promoter activity. Mutation constructs of the CTLA4 promoter uncover an enhancer binding site located within the -150 to -130 bp region relative to the transcription start site. Promoter analysis and chromatin immunoprecipitation assays suggest that cAMP response element-binding is a putative transcription factor induced by cAMP. We have previously shown that CTLA4 mediates decreased pulmonary inflammation in an LPS-induced murine model of acute lung injury (ALI). We observed that LPS can induce CTLA4 transcription via the same cAMP-inducible promoter region. The immunosuppressant, rapamycin, decreases cAMP and LPS-induced CTLA4 transcription in vitro. In vivo, LPS induces cAMP accumulation in bronchoalveolar lavage fluid, bronchoalveolar lavage cells, and lung tissues in ALI. We demonstrate that rapamycin decreases cAMP accumulation and CTLA4 expression in ALI. Together, these data suggest that cAMP may negatively regulate pulmonary inflammatory responses in vivo and in vitro by altering CTLA4 expression.

Mucin granule-associated proteins in human bronchial epithelial cells: the airway goblet cell "granulome".

BACKGROUND: Excess mucus in the airways leads to obstruction in diseases such as chronic bronchitis, asthma, and cystic fibrosis. Mucins, the highly glycosolated protein components of mucus, are stored in membrane-bound granules housed in the cytoplasm of airway epithelial "goblet" cells until they are secreted into the airway lumen via an exocytotic process. Precise mechanism(s) of mucin secretion, including the specific proteins involved in the process, have yet to be elucidated. Previously, we have shown that the Myristoylated Alanine-Rich C Kinase Substrate (MARCKS) protein regulates mucin secretion by orchestrating translocation of mucin granules from the cytosol to the plasma membrane, where the granules dock, fuse and release their contents into the airway lumen. Associated with MARCKS in this process are chaperone (Heat Shock Protein 70 [HSP70], Cysteine string protein [CSP]) and cytoskeletal (actin, myosin) proteins. However, additional granule-associated proteins that may be involved in secretion have not yet been elucidated. METHODS: Here, we isolated mucin granules and granule membranes from primary cultures of well differentiated human bronchial epithelial cells utilizing a novel technique of immuno-isolation, based on the presence of the calcium activated chloride channel hCLCA1 (the human ortholog of murine Gob-5) on the granule membranes, and verified via Western blotting and co-immunoprecipitation that MARCKS, HSP70, CSP and hCLCA1 were present on the granule membranes and associated with each other. We then subjected the isolated granules/membranes to liquid chromatography mass spectrometry (LC-MS/MS) to identify other granule associated proteins. RESULTS: A number of additional cytoskeletal (e.g. Myosin Vc) and regulatory proteins (e.g. Protein phosphatase 4) associated with the granules and could play a role in secretion were discovered. This is the first description of the airway goblet cell "granulome."

Emerging pathways in asthma: innate and adaptive interactions.

BACKGROUND: Allergic asthma is a complex and chronic airway inflammatory disorder, and the prevalence of asthma has increased. Adaptive antigen-dependent immunity is a classical pathway of asthmatic pathology. Recent studies have focused on innate antigen-independent immunity in asthma. SCOPE OF REVIEW: This review discusses updated research associating innate immunity with allergic asthma. We focus on innate molecules (Toll-like receptors and nucleotide-binding oligomerization domain-like receptors) and review studies regarding innate and adaptive interactions in allergic responses (surfactant protein D, lipopolysaccharide, and early life immune responses). We also highlight new emerging concepts in the field applicable to innate immunity and asthma. MAJOR CONCLUSIONS: Innate immunity plays a key role in asthma. Understanding innate and adaptive interactions provide significant information in asthmatic research. Innate molecules not only contribute to classical pulmonary defense, but also modulate inflammatory responses. Emerging concepts in the analysis of the microbiome, microRNA and autophagy may provide new insights in searching therapeutic targets. GENERAL SIGNIFICANCE: Finding specific mechanisms of innate and/or adaptive immunity in asthma are timely goals for further research. Integration of bioinformatics and systems biology tools, particularly in relation to microbiome analysis, may be helpful in providing an understanding to allergic immune responses. This article is part of a Special Issue entitled Biochemistry of Asthma.

Surfactant protein D-mediated decrease of allergen-induced inflammation is dependent upon CTLA4.

Pulmonary surfactant protein D (SP-D), a member of the collectin family, is an innate immune molecule critical for defense that can also modulate adaptive immune responses. We previously showed that SP-D-deficient mice exhibit enhanced allergic responses and that SP-D induction requires lymphocytes. Thus, we postulated that SP-D may decrease adaptive allergic responses through interaction with T cells. In this study, we used two forms of SP-D, a dodecamer and a shorter fragment containing the trimeric neck and carbohydrate recognition domains (SP-D NCRD). Both forms decreased immune responses in vitro and in a murine model of pulmonary inflammation. SP-D NCRD increased transcription of CTLA4, a negative regulator of T cell activation, in T cells. SP-D NCRD no longer decreased lymphoproliferation and IL-2 cytokine production when CTLA4 signals were abrogated. Administration of SP-D NCRD in vivo no longer decreased allergen induced responses when CTLA4 was inhibited. Our results indicate that SP-D decreases allergen responses, an effect that may be mediated by increase of CTLA4 in T cells.

T cell pathways involving CTLA4 contribute to a model of acute lung injury.

Acute lung injury (ALI) is a frequent pulmonary complication in critically ill patients. We characterized a murine model of LPS-induced ALI, focusing on Th cells. Following LPS administration, bronchoalveolar lavage lymphocytes, neutrophils, IL-6, TNF-alpha, and albumin were increased. Analysis of LPS-induced T cells revealed increased Th cell-associated cytokines (IL-17A, -17F, and -22), as well as increased expression of CD69 (a cell activation marker), Foxp3, and CTLA4 in CD4(+) T cells. Administration of anti-CTLA4 Ab decreased LPS-induced bronchoalveolar lavage albumin and IL-17A, while increasing CD4(+)Foxp3(+) cell number and Foxp3 expression in CD4(+)Foxp3(+) cells. These data suggest that pulmonary LPS administration promotes CD4(+) T cells and that T cell pathways involving CTLA4 contribute to ALI.

MARCKS and related chaperones bind to unconventional myosin V isoforms in airway epithelial cells.

We have shown previously that myristoylated alanine-rich C kinase substrate (MARCKS) is a key regulatory molecule in the process of mucin secretion by airway epithelial cells, and that part of the secretory mechanism involves intracellular associations of MARCKS with specific chaperones: heat shock protein 70 (Hsp70) and cysteine string protein (CSP). Here, we report that MARCKS also interacts with unconventional myosin isoforms within these cells, and further molecular interactions between MARCKS and these chaperones/cytoskeletal proteins are elucidated. Primary human bronchial epithelial cells and the HBE1 cell line both expressed myosin V and VI proteins, and both MARCKS and CSP were shown to bind to myosin V, specifically Va and Vc. This binding was enhanced by exposing the cells to phorbol-12-myristate-13-acetate, an activator of protein kinase C and stimulator of mucin secretion. Binding of MARCKS, Hsp70, and CSP was further investigated by His-tagged pull down assays of purified recombinant proteins and multiple transfections of HBE1 cells with fusion proteins (MARCKS-HA; Flag-Hsp70; c-Myc-CSP) and immunoprecipitation. The results showed that MARCKS binds directly to Hsp70, and that Hsp70 binds directly to CSP, but that MARCKS binding to CSP appears to require the presence of Hsp70. Interrelated binding(s) of MARCKS, chaperones, and unconventional myosin isoforms may be integral to the mucin secretion process.

MARCKS regulation of mucin secretion by airway epithelium in vitro: interaction with chaperones.

We have reported previously that myristoylated alanine-rich C kinase substrate (MARCKS) is a key regulatory molecule controlling mucin secretion by airway epithelial cells in vitro and in vivo. The results of those studies supported a mechanism whereby MARCKS, upon phosphorylation by protein kinase C (PKC), translocates from plasma membrane to cytoplasm, where its binding to membranes of intracellular mucin granules is a key component of the secretory pathway. It remains unknown how MARCKS is targeted to and/or preferentially attaches to mucin granule membranes. We hypothesized that the chaperone cysteine string protein (CSP) may play an important role in this process. CSP was shown to associate with membranes of intracellular mucin granules in well-differentiated normal human bronchial epithelial (NHBE) cells in vitro, as determined by ultrastructural immunohistochemistry and Western blotting of isolated granule membranes. CSP in these cells complexed with MARCKS, as shown by co-immunoprecipitation. Given reported associations between CSP and a second chaperone, heat shock protein 70 (HSP70), a role for HSP70 in the MARCKS-dependent secretory mechanism also was investigated. HSP70 appeared to form a trimeric complex with MARCKS and CSP associated with mucin granule membranes within airway epithelial cells. Transfection of the HBE1 human bronchial epithelial cell line with siRNAs targeting sequences of MARCKS, CSP, or HSP70 resulted, in each case, in significant knockdown of expression of these proteins and subsequent attenuation of mucin secretion. The results provide the first evidence that CSP and HSP70, and their interactions with MARCKS, are involved in mucin secretion.

Protease-activated receptor-2 (PAR-2) is a weak enhancer of mucin secretion by human bronchial epithelial cells in vitro.

PAR-2, a member of a family of G-protein-coupled receptors, can be activated by serine proteases via proteolytic cleavage. PAR-2 expression is known to be upregulated in respiratory epithelium subsequent to inflammation in asthma and chronic obstructive pulmonary disease (COPD). Since these diseases also are characterized by excessive mucus production and secretion, we investigated whether PAR-2 could be linked to mucin hypersecretion by airway epithelium. Normal human bronchial epithelial (NHBE) cells in primary culture or the human bronchial epithelial cell lines, NCI-H292 and HBE-1, were used. NHBE, NCI-H292, and HBE-1 cells expressed prominent levels of PAR-2 protein. Short-term (30min) exposure of cells to the synthetic PAR-2 agonist peptide (SLIGKV-NH2) elicited a small but statistically significant increase in mucin secretion at high concentrations (100microM and 1000microM), compared to a control peptide with reversed amino acid sequence (VKGILS-NH2). Neither human lung tryptase nor bovine pancreatic trypsin, both PAR-2 agonists, affected NHBE cell mucin secretion when added over a range of concentrations. Knockdown of PAR-2 expression by siRNA blocked the stimulatory effect of the AP. The results suggest that, since PAR-2 activation only weakly increases mucin secretion by human airway epithelial cells in vitro, PAR-2 probably is not a significant contributor to mucin hypersecretion in inflamed airways.