reComBat: Batch effect removal in large-scale, multi-source omics data integration

With the steadily increasing abundance of omics data produced all over the world, some-times decades apart and under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch effect removal for entire databases lies in the large number and coincide of both batches and desired, biological variation resulting in design matrix singularity. This problem currently cannot be solved by any common batch correction algorithm. In this study, we present reComBat , a regularised version of the empirical Bayes method to overcome this limitation. We demonstrate our approach for the harmonisation of public gene expression data of the human opportunistic pathogen Pseudomonas aeruginosa and study a several metrics to empirically demonstrate that batch effects are successfully mitigated while biologically meaningful gene expression variation is retained. reComBat fills the gap in batch correction approaches applicable to large scale, public omics databases and opens up new avenues for data driven analysis of complex biological processes beyond the scope of a single study

Electromagnetic properties of non-Dirac particles with rest spin 1/2

We resolve a number of questions related to an analytic description of electromagnetic form factors of non-Dirac particles with the rest spin 1/2. We find the general structure of a matrix antisymmetric tensor operator. We obtain two recurrence relations for matrix elements of finite transformations of the proper Lorentz group and explicit formulas for a certain set of such elements. Within the theory of fields with double symmetry, we discuss writing the components of wave vectors of particles in the form of infinite continued fractions. We show that for $Q^{2} \leq 0.5$ (GeV/c)$^{2}$, where $Q^{2}$ is the transferred momentum squared, electromagnetic form factors that decrease as $Q^{2}$ increases and are close to those experimentally observed in the proton can be obtained without explicitly introducing an internal particle structure.Comment: 18 pages, 2 figure

Stacking faults and superstructures in a layered brownmillerite

Stacking faults in Ca4Fe2Mn0.5Ti0.5O9 have been examined using X-ray diffraction and high-resolution transmission electron microscopy. Electron diffraction revealed two superstructures with ordered stacking sequences

Internally Electrodynamic Particle Model: Its Experimental Basis and Its Predictions

The internally electrodynamic (IED) particle model was derived based on overall experimental observations, with the IED process itself being built directly on three experimental facts, a) electric charges present with all material particles, b) an accelerated charge generates electromagnetic waves according to Maxwell's equations and Planck energy equation and c) source motion produces Doppler effect. A set of well-known basic particle equations and properties become predictable based on first principles solutions for the IED process; several key solutions achieved are outlined, including the de Broglie phase wave, de Broglie relations, Schr\"odinger equation, mass, Einstein mass-energy relation, Newton's law of gravity, single particle self interference, and electromagnetic radiation and absorption; these equations and properties have long been broadly experimentally validated or demonstrated. A specific solution also predicts the Doebner-Goldin equation which emerges to represent a form of long-sought quantum wave equation including gravity. A critical review of the key experiments is given which suggests that the IED process underlies the basic particle equations and properties not just sufficiently but also necessarily.Comment: Presentation at the 27th Int Colloq on Group Theo Meth in Phys, 200

Social interaction patterns, therapist responsiveness, and outcome in treatments for borderline personality disorder.

Inflexible social interaction patterns are defining features of borderline personality disorder (BPD). Specific beliefs about the self and others may be activated across interaction situations, often leading to instable relationships. It may be pivotal to address these difficulties in early treatment phases, through appropriate therapist responsiveness, which means an adaptation of therapist's activity to their client's behaviours using emerging information in the process (Stiles, 2009, Clinical Psychology: Science and Practice, 16, 86). In this process-outcome study, responsiveness is operationalized by the motive-oriented therapeutic relationship (Caspar, 2007, Handbook of psychotherapeutic case formulations, 2nd ed., 251-289, Guilford), based on the Plan analysis case formulation. The present study assesses the interplay between social interaction problems and therapist responsiveness, explaining symptoms at discharge and the therapeutic alliance. In total, N = 50 clients with BPD entered the study, and standard and responsive treatments were compared. Social interaction patterns were assessed by the newly developed Borderline Interaction Patterns Scale (BIPS), applied to recorded material of three sessions per therapy. Outcome was measured by general symptoms (OQ-45), borderline symptoms (BSL-23), interpersonal problems (IIP), and the therapeutic alliance (WAI). Results suggest that in standard treatment, social interaction patterns are neither related to outcome nor the therapeutic alliance. In responsive treatment, more activation of social interaction patterns predicted better outcome on IIP and lower therapist ratings of the alliance. The conclusions seem promising for specific effectiveness of responsive treatments in particular in the interpersonal problem area of BPD. Identifying social interaction patterns early in treatment may be a crucial pathway to change for BPD. Responsive therapy activating social interaction patterns may be crucial for better outcome. Future research should focus on mechanisms of change in early treatment phases for BPD. New scale for assessing social interaction patterns specific to borderline personality disorder

Supersymmetric QCD corrections to e+e−→tbˉH−e^+e^-\to t\bar{b}H^- and the Bernstein-Tkachov method of loop integration

The discovery of charged Higgs bosons is of particular importance, since their existence is predicted by supersymmetry and they are absent in the Standard Model (SM). If the charged Higgs bosons are too heavy to be produced in pairs at future linear colliders, single production associated with a top and a bottom quark is enhanced in parts of the parameter space. We present the next-to-leading-order calculation in supersymmetric QCD within the minimal supersymmetric SM (MSSM), completing a previous calculation of the SM-QCD corrections. In addition to the usual approach to perform the loop integration analytically, we apply a numerical approach based on the Bernstein-Tkachov theorem. In this framework, we avoid some of the generic problems connected with the analytical method.Comment: 14 pages, 6 figures, accepted for publication in Phys. Rev.