NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery.

Major histocompatibility complex class I (MHC-I) molecules play an essential role in the cellular immune response, presenting peptides to cytotoxic T lymphocytes (CTLs) allowing the immune system to scrutinize ongoing intracellular production of proteins. In the early 1990s, immunogenicity and stability of the peptide-MHC-I (pMHC-I) complex were shown to be correlated. At that time, measuring stability was cumbersome and time consuming and only small data sets were analysed.

Differential brain response to alcohol cue distractors across stages of alcohol dependence.

Altered attention to alcohol-related cues is implicated in the craving and relapse cycle characteristic of alcohol dependence (ALC). Prior cue reactivity studies typically invoke explicit attention to alcohol cues, so the neural response underlying incidental cue exposure remains unclear. Here, we embed infrequent, task-irrelevant alcohol and non-alcohol cues in an attention-demanding task, enabling evaluation of brain responses to distracting alcohol cues.

Model selection for Gaussian kernel PCA denoising.

We propose kernel parallel analysis (kPA) for automatic kernel scale and model order selection in Gaussian kernel principal component analysis (KPCA). Parallel analysis is based on a permutation test for covariance and has previously been applied for model order selection in linear PCA, we here augment the procedure to also tune the Gaussian kernel scale of radial basis function based KPCA. We evaluate kPA for denoising of simulated data and the U.

Structural properties of MHC class II ligands, implications for the prediction of MHC class II epitopes.

Major Histocompatibility class II (MHC-II) molecules sample peptides from the extracellular space allowing the immune system to detect the presence of foreign microbes from this compartment. Prediction of MHC class II ligands is complicated by the open binding cleft of the MHC class II molecule, allowing binding of peptides extending out of the binding groove. Furthermore, only a few HLA-DR alleles have been characterized with a sufficient number of peptides (100-200 peptides per allele) to derive accurate description of their binding motif.

Multisite reliability of cognitive BOLD data.

Investigators perform multi-site functional magnetic resonance imaging studies to increase statistical power, to enhance generalizability, and to improve the likelihood of sampling relevant subgroups. Yet undesired site variation in imaging methods could off-set these potential advantages. We used variance components analysis to investigate sources of variation in the blood oxygen level-dependent (BOLD) signal across four 3-T magnets in voxelwise and region-of-interest (ROI) analyses.

Error detection failures in schizophrenia: ERPs and FMRI.

Self-monitoring of actions, critical for guiding goal-directed behavior, is deficient in schizophrenia. Defective error-monitoring may reflect more general self-monitoring deficiencies. Prior studies have shown that the error-related negativity (ERN) component of the event-related potential (ERP) is smaller in patients with schizophrenia.

Tuning in to the voices: a multisite FMRI study of auditory hallucinations.

Introduction: Auditory hallucinations or voices are experienced by 75% of people diagnosed with schizophrenia. We presumed that auditory cortex of schizophrenia patients who experience hallucinations is tonically "tuned" to internal auditory channels, at the cost of processing external sounds, both speech and nonspeech. Accordingly, we predicted that patients who hallucinate would show less auditory cortical activation to external acoustic stimuli than patients who did not.