A Beginners Guide to Factor Analysis: Focusing on Exploratory Factor Analysis

The following paper discusses exploratory factor analysis and gives an overview of the statistical technique and how it is used in various research designs and applications. A basic outline of how the technique works and its criteria, including its main assumptions are discussed as well as when it should be used. Mathematical theories are explored to enlighten students on how exploratory factor analysis works, an example of how to run an exploratory factor analysis on SPSS is given, and finally a section on how to write up the results is provided. This will allow readers to develop a better understanding of when to employ factor analysis and how to interpret the tables and graphs in the output

Adenosine-mono-phosphate-activated protein kinase-independent effects of metformin in T cells

The anti-diabetic drug metformin regulates T-cell responses to immune activation and is proposed to function by regulating the energy-stress-sensing adenosine-monophosphate-activated protein kinase (AMPK). However, the molecular details of how metformin controls T cell immune responses have not been studied nor is there any direct evidence that metformin acts on T cells via AMPK. Here, we report that metformin regulates cell growth and proliferation of antigen-activated T cells by modulating the metabolic reprogramming that is required for effector T cell differentiation. Metformin thus inhibits the mammalian target of rapamycin complex I signalling pathway and prevents the expression of the transcription factors c-Myc and hypoxia-inducible factor 1 alpha. However, the inhibitory effects of metformin on T cells did not depend on the expression of AMPK in T cells. Accordingly, experiments with metformin inform about the importance of metabolic reprogramming for T cell immune responses but do not inform about the importance of AMPK

Engineering Proteinase Inihibitor Genes For Plant Defense Against Predators

Small proteinaceous inhibitors (Mr\u3c20,000) of the digestive serine proteinases of animals and microorganisms are found as moderately abundant proteins in storage organs and leaves of many plant genera. The proteins are powerful inhibitors of the digestive enzymes of plant predators and therefore are considered to be part of the array of defensive chemicals of plants. Proteinase inhibitor genes show excellent promise, using DNA technology, to manipulate plant genomes to express these biologically active proteins in order to improve natural defense systems. Members of two unrelated families of serine proteinase inhibitors found in tomato and potato plants, called Inhibitor I (monomer Mr 8000) and Inhibitor II (monomer Mr 12,300), are under both environmental and developmental regulation in different tissues of the plants. Genes coding for wound-inducible Inhibitors I and II have been isolated from both tomato and potato genomes and characterized. Tobacco plants have been transformed with the chimeric genes containing wound-inducible promoters fused with the reporter gene, chloramphenicol acetyl transferase, to assess promoter function and signal transmission. Transacting factors that regulate their expression in response to wounding are also being identified and purified. Intact genes are being employed to transform agriculturally important crop plants to determine their potential usefulness to enhance defensive capabilities of plants against herbivores and pathogens

Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings

Recently, evidence has emerged that humans approach learning using Bayesian updating rather than (model-free) reinforcement algorithms in a six-arm restless bandit problem. Here, we investigate what this implies for human appreciation of uncertainty. In our task, a Bayesian learner distinguishes three equally salient levels of uncertainty. First, the Bayesian perceives irreducible uncertainty or risk: even knowing the payoff probabilities of a given arm, the outcome remains uncertain. Second, there is (parameter) estimation uncertainty or ambiguity: payoff probabilities are unknown and need to be estimated. Third, the outcome probabilities of the arms change: the sudden jumps are referred to as unexpected uncertainty. We document how the three levels of uncertainty evolved during the course of our experiment and how it affected the learning rate. We then zoom in on estimation uncertainty, which has been suggested to be a driving force in exploration, in spite of evidence of widespread aversion to ambiguity. Our data corroborate the latter. We discuss neural evidence that foreshadowed the ability of humans to distinguish between the three levels of uncertainty. Finally, we investigate the boundaries of human capacity to implement Bayesian learning. We repeat the experiment with different instructions, reflecting varying levels of structural uncertainty. Under this fourth notion of uncertainty, choices were no better explained by Bayesian updating than by (model-free) reinforcement learning. Exit questionnaires revealed that participants remained unaware of the presence of unexpected uncertainty and failed to acquire the right model with which to implement Bayesian updating

In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers

The search for druggable pockets on the surface of a protein is often performed on a single conformer, treated as a rigid body. Transient druggable pockets may be missed in this approach. Here, we describe a methodology for systematic in silico analysis of surface clefts across multiple conformers of the metastable protein α1-antitrypsin (A1AT). Pathological mutations disturb the conformational landscape of A1AT, triggering polymerisation that leads to emphysema and hepatic cirrhosis. Computational screens for small molecule inhibitors of polymerisation have generally focused on one major druggable site visible in all crystal structures of native A1AT. In an alternative approach, we scan all surface clefts observed in crystal structures of A1AT and in 100 computationally produced conformers, mimicking the native solution ensemble. We assess the persistence, variability and druggability of these pockets. Finally, we employ molecular docking using publicly available libraries of small molecules to explore scaffold preferences for each site. Our approach identifies a number of novel target sites for drug design. In particular one transient site shows favourable characteristics for druggability due to high enclosure and hydrophobicity. Hits against this and other druggable sites achieve docking scores corresponding to a Kd in the µM–nM range, comparing favourably with a recently identified promising lead. Preliminary ThermoFluor studies support the docking predictions. In conclusion, our strategy shows considerable promise compared with the conventional single pocket/single conformer approach to in silico screening. Our best-scoring ligands warrant further experimental investigation

PAMELA results on the cosmic-ray antiproton flux from 60 MeV to 180 GeV in kinetic energy

The satellite-borne experiment PAMELA has been used to make a new measurement of the cosmic-ray antiproton flux and the antiproton-to-proton flux ratio which extends previously published measurements down to 60 MeV and up to 180 GeV in kinetic energy. During 850 days of data acquisition approximately 1500 antiprotons were observed. The measurements are consistent with purely secondary production of antiprotons in the galaxy. More precise secondary production models are required for a complete interpretation of the results.Comment: 11 pages, 3 figures, 1 table. Accepted for publication in Physical Review Letter

Deducing the source and composition of rare earth mineralising fluids in carbonatites: insights from isotopic (C, O, 87Sr/86Sr) data from Kangankunde, Malawi

This is the final version of the article. Available from Springer Verlag via the DOI in this record.Carbonatites host some of the largest and highest grade rare earth element (REE) deposits but the composition and source of their REE-mineralising fluids remains enigmatic. Using C, O and 87Sr/86Sr isotope data together with major and trace element compositions for the REE-rich Kangankunde carbonatite (Malawi), we show that the commonly observed, dark brown, Fe-rich carbonatite that hosts REE minerals in many carbonatites is decoupled from the REE mineral assemblage. REE-rich ferroan dolomite carbonatites, containing 8–15 wt% REE2O3, comprise assemblages of monazite-(Ce), strontianite and baryte forming hexagonal pseudomorphs after probable burbankite. The 87Sr/86Sr values (0.70302–0.70307) affirm a carbonatitic origin for these pseudomorph-forming fluids. Carbon and oxygen isotope ratios of strontianite, representing the REE mineral assemblage, indicate equilibrium between these assemblages and a carbonatite-derived, deuteric fluid between 250 and 400 °C (δ18O + 3 to + 5‰VSMOW and δ13C − 3.5 to − 3.2‰VPDB). In contrast, dolomite in the same samples has similar δ13C values but much higher δ18O, corresponding to increasing degrees of exchange with low-temperature fluids (< 125 °C), causing exsolution of Fe oxides resulting in the dark colour of these rocks. REE-rich quartz rocks, which occur outside of the intrusion, have similar δ18O and 87Sr/86Sr to those of the main complex, indicating both are carbonatite-derived and, locally, REE mineralisation can extend up to 1.5 km away from the intrusion. Early, REE-poor apatite-bearing dolomite carbonatite (beforsite: δ18O + 7.7 to + 10.3‰ and δ13C −5.2 to −6.0‰; 87Sr/86Sr 0.70296–0.70298) is not directly linked with the REE mineralisation.This project was funded by the UK Natural Environment Research Council (NERC) SoS RARE project (NE/M011429/1) and by NIGL (NERC Isotope Geoscience Laboratory) Project number 20135

Axial forces and bending moments in the loaded rabbit tibia in vivo

<p>Abstract</p> <p>Background</p> <p>Different animal models are used as fracture models in orthopaedic research prior to implant use in humans, although biomechanical forces can differ to a great extend between species due to variable anatomic conditions, particularly with regard to the gait. The rabbit is an often used fracture model, but biomechanical data are very rare. The objective of the present study was to measure axial forces, bending moments, and bending axis directly in the rabbit tibia <it>in vivo</it>. The following hypothesis was tested: Axial forces and bending moments in the mid-diaphysis of rabbit tibia differ from other experimental animals or indirectly calculated data.</p> <p>Methods</p> <p>A minifixateur system with 4 force sensors was developed and attached to rabbit tibia (<it>n </it>= 4), which were subsequently ostectomised. Axial forces, bending moments and bending angles were calculated telemetrically during weight bearing in motion between 6 and 42 days post operation.</p> <p>Results</p> <p>Highest single values were 201% body weight [% bw] for axial forces and 409% bw cm for bending moments. Whereas there was a continous decrease in axial forces over time after day 10 (<it>P </it>= 0.03 on day 15), a decrease in bending moments was inconsistent (<it>P </it>= 0.03 on day 27). High values for bending moments were frequently, but not consistently, associated with high values for axial forces.</p> <p>Conclusion</p> <p>Axial forces in rabbit tibia exceeded axial forces in sheep, and differed from indirectly calculated data. The rabbit is an appropriate fracture model because axial loads and bending moments in rabbit tibia were more closely to human conditions than in sheep tibia as an animal model.</p

Sugary interfaces mitigate contact damage where stiff meets soft

The byssal threads of the fan shell Atrina pectinata are non-living functional materials intimately associated with living tissue, which provide an intriguing paradigm of bionic interface for robust load-bearing device. An interfacial load-bearing protein (A. pectinata foot protein-1, apfp-1) with L-3,4-dihydroxyphenylalanine (DOPA)-containing and mannose-binding domains has been characterized from Atrina's foot. apfp-1 was localized at the interface between stiff byssus and the soft tissue by immunochemical staining and confocal Raman imaging, implying that apfp-1 is an interfacial linker between the byssus and soft tissue, that is, the DOPA-containing domain interacts with itself and other byssal proteins via Fe3(+)-DOPA complexes, and the mannose-binding domain interacts with the soft tissue and cell membranes. Both DOPA-and sugar-mediated bindings are reversible and robust under wet conditions. This work shows the combination of DOPA and sugar chemistry at asymmetric interfaces is unprecedented and highly relevant to bionic interface design for tissue engineering and bionic devices

Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis

Allergic rhinitis is the most common clinical presentation of allergy, affecting 400 million people worldwide, with increasing incidence in westernized countries1,2. To elucidate the genetic architecture and understand the underlying disease mechanisms, we carried out a meta-analysis of allergic rhinitis in 59,762 cases and 152,358 controls of European ancestry and identified a total of 41 risk loci for allergic rhinitis, including 20 loci not previously associated with allergic rhinitis, which were confirmed in a replication phase of 60,720 cases and 618,527 controls. Functional annotation implicated genes involved in various immune pathways, and fine mapping of the HLA region suggested amino acid variants important for antigen binding. We further performed genome-wide association study (GWAS) analyses of allergic sensitization against inhalant allergens and nonallergic rhinitis, which suggested shared genetic mechanisms across rhinitis-related traits. Future studies of the identified loci and genes might identify novel targets for treatment and prevention of allergic rhinitis