Neuroimaging and neuropsychological studies have suggested that common features characterize both Gambling Disorder (GD) and Alcohol Use Disorder (AUD), but these conditions have rarely been compared.

To increase power when analyzing fMRI data, researchers often define functional regions of interest (fROIs). It is crucial that this fROI is defined with an optimal balance between both false positives and false negatives to ensure maximal spatial accuracy and to avoid potentially biased results in the main fMRI experiment. Additionally, since the fROI is defined in each subject separately, the used method should attune to the general level of activation of the individual.

Functional features of synaptic populations are typically inferred from random electrophysiological sampling of small subsets of synapses. Are these samples unbiased? Here, we develop a biophysically constrained statistical framework to address this question and apply it to assess the performance of a widely used method based on a failure-rate analysis to quantify the occurrence of silent (AMPAR-lacking) synapses. We simulate this method in silico and find that it is characterized by strong and systematic biases, poor reliability, and weak statistical power. Key conclusions are validated by whole-cell recordings from hippocampal neurons. To address these shortcomings, we develop a simulator of the experimental protocol and use it to compute a synthetic likelihood. By maximizing the likelihood, we infer silent synapse fraction with no bias, low variance, and superior statistical power over alternatives. Together, this generalizable approach highlights how a simulator of experimental methodologies can substantially improve the estimation of physiological properties.

Quantitative data analysis is important for any single-molecule localization microscopy (SMLM) workflow to extract biological insights from the coordinates of the single fluorophores. However, current approaches are restricted to simple geometries or require identical structures. Here, we present LocMoFit (Localization Model Fit), an open-source framework to fit an arbitrary model to localization coordinates. It extracts meaningful parameters from individual structures and can select the most suitable model. In addition to analyzing complex, heterogeneous and dynamic structures for in situ structural biology, we demonstrate how LocMoFit can assemble multi-protein distribution maps of six nuclear pore components, calculate single-particle averages without any assumption about geometry or symmetry, and perform a time-resolved reconstruction of the highly dynamic endocytic process from static snapshots. We provide extensive simulation and visualization routines to validate the robustness of LocMoFit and tutorials to enable any user to increase the information content they can extract from their SMLM data.

Protein complexes participate in many important cellular functions, so finding the set of existent complexes is essential for understanding the organization and regulation of processes in the cell. With the availability of large amounts of high-throughput protein-protein interaction (PPI) data, many algorithms have been proposed to discover protein complexes from PPI networks. However, such approaches are hindered by the high rate of noise in high-throughput PPI data, including spurious and missing interactions. Furthermore, many transient interactions are detected between proteins that are not from the same complex, while not all proteins from the same complex may actually interact. As a result, predicted complexes often do not match true complexes well, and many true complexes go undetected.

The purpose of this work is to present a computer assisted diagnostic tool for radiologists in their diagnosis of Alzheimer's disease. A statistical likelihood-ratio procedure from signal detection theory was implemented in the detection of Alzheimer's disease. The probability density functions of the likelihood ratio were constructed by using medial temporal lobe (MTL) volumes of patients with Alzheimer's disease (AD) and normal controls (NC). The volumes of MTL as well as other anatomical regions of the brains were calculated by the FreeSurfer software using T1 weighted MRI images. The MRI images of AD and NC were downloaded from the database of Alzheimer's disease neuroimaging initiative (ADNI). A separate dataset of minimal interval resonance imaging in Alzheimer's disease (MIRIAD) was used for diagnostic testing. A sensitivity of 89.1% and specificity of 87.0% were achieved for the MIRIAD dataset which are better than the 85% sensitivity and specificity achieved by the best radiologists without input of other patient information.

Formal thought disorder (FTD) refers to a psychopathological dimension characterized by disorganized and incoherent speech. Whether symptoms of FTD arise from aberrant processing in language-related regions or more general cognitive networks, however, remains debated. Here, we addressed this question by a quantitative meta-analysis of published functional neuroimaging studies on FTD. The revised Activation Likelihood Estimation (ALE) algorithm was used to test for convergent aberrant activation changes in 18 studies (30 experiments) investigating FTD, of which 17 studies comprised schizophrenia patients and one study healthy subjects administered to S-ketamine. Additionally, we analyzed task-dependent and task-independent (resting-state) functional connectivity (FC) of brain regions showing convergence in activation changes. Subsequent functional characterization was performed for the initial clusters and the delineated connectivity networks by reference to the BrainMap database. Consistent activation changes were found in the left superior temporal gyrus (STG) and two regions within the left posterior middle temporal gyrus (p-MTG), ventrally (vp-MTG) and dorsally (dp-MTG). Functional characterization revealed a prominent functional association of ensuing clusters from our ALE meta-analysis with language and speech processing, as well as auditory perception in STG and with social cognition in dp-MTG. FC analysis identified task-dependent and task-independent networks for all three seed regions, which were mainly related to language and speech processing, but showed additional involvement in higher order cognitive functions. Our findings suggest that FTD is mainly characterized by abnormal activation in brain regions of the left hemisphere that are associated with language and speech processing, but also extend to higher order cognitive functions. Hum Brain Mapp 38:4946-4965, 2017. © 2017 Wiley Periodicals, Inc.

Current early risk stratification of coronary artery disease (CAD) consists of pre-test probability scoring such as the 2019 ESC guidelines on chronic coronary syndromes (ESC2019), which has low specificity and thus rule-out capacity. A newer clinical risk factor model (risk factor-weighted clinical likelihood, RF-CL) showed significantly improved rule-out capacity over the ESC2019 model. The aim of the current study was to investigate if the addition of acoustic features to the RF-CL model could improve the rule-out potential of the best performing clinical risk factor models.

Multisensory perception is regarded as one of the most prominent examples where human behaviour conforms to the computational principles of maximum likelihood estimation (MLE). In particular, observers are thought to integrate auditory and visual spatial cues weighted in proportion to their relative sensory reliabilities into the most reliable and unbiased percept consistent with MLE. Yet, evidence to date has been inconsistent. The current pre-registered, large-scale (N = 36) replication study investigated the extent to which human behaviour for audiovisual localization is in line with maximum likelihood estimation. The acquired psychophysics data show that while observers were able to reduce their multisensory variance relative to the unisensory variances in accordance with MLE, they weighed the visual signals significantly stronger than predicted by MLE. Simulations show that this dissociation can be explained by a greater sensitivity of standard estimation procedures to detect deviations from MLE predictions for sensory weights than for audiovisual variances. Our results therefore suggest that observers did not integrate audiovisual spatial signals weighted exactly in proportion to their relative reliabilities for localization. These small deviations from the predictions of maximum likelihood estimation may be explained by observers' uncertainty about the world's causal structure as accounted for by Bayesian causal inference.

Plant root systems play vital roles in the biosphere, environment and agriculture, but the quantitative principles governing their growth and architecture remain poorly understood. The 'forward problem' of what root forms can arise from given models and parameters has been well studied through modelling and simulation, but comparatively little attention has been given to the 'inverse problem': what models and parameters are responsible for producing an experimentally observed root system? Here, we propose the use of approximate Bayesian computation (ABC) to infer mechanistic parameters governing root growth and architecture, allowing us to learn and quantify uncertainty in parameters and model structures using observed root architectures. We demonstrate the use of this platform on synthetic and experimental root data and show how it may be used to identify growth mechanisms and characterize growth parameters in different mutants. Our highly adaptable framework can be used to gain mechanistic insight into the generation of observed root system architectures.

The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely.

It has been suggested that the simulation of hypothetical episodes and the recollection of past episodes are supported by fundamentally the same set of brain regions. The present article specifies this core network via Activation Likelihood Estimation (ALE). Specifically, a first meta-analysis revealed joint engagement of expected core-network regions during episodic memory and episodic simulation. These include parts of the medial surface, the hippocampus and parahippocampal cortex within the medial temporal lobes, and the temporal and inferior posterior parietal cortices on the lateral surface. Both capacities also jointly recruited additional regions such as parts of the bilateral dorsolateral prefrontal cortex. All of these core regions overlapped with the default network. Moreover, it has further been suggested that episodic simulation may require a stronger engagement of some of the core network's nodes as well as the recruitment of additional brain regions supporting control functions. A second ALE meta-analysis indeed identified such regions that were consistently more strongly engaged during episodic simulation than episodic memory. These comprised the core-network clusters located in the left dorsolateral prefrontal cortex and posterior inferior parietal lobe and other structures distributed broadly across the default and fronto-parietal control networks. Together, the analyses determine the set of brain regions that allow us to experience past and hypothetical episodes, thus providing an important foundation for studying the regions' specialized contributions and interactions.

The vestibular system contributes to the control of posture and eye movements and is also involved in various cognitive functions including spatial navigation and memory. These functions are subtended by projections to a vestibular cortex, whose exact location in the human brain is still a matter of debate (Lopez and Blanke, 2011). The vestibular cortex can be defined as the network of all cortical areas receiving inputs from the vestibular system, including areas where vestibular signals influence the processing of other sensory (e.g. somatosensory and visual) and motor signals. Previous neuroimaging studies used caloric vestibular stimulation (CVS), galvanic vestibular stimulation (GVS), and auditory stimulation (clicks and short-tone bursts) to activate the vestibular receptors and localize the vestibular cortex. However, these three methods differ regarding the receptors stimulated (otoliths, semicircular canals) and the concurrent activation of the tactile, thermal, nociceptive and auditory systems. To evaluate the convergence between these methods and provide a statistical analysis of the localization of the human vestibular cortex, we performed an activation likelihood estimation (ALE) meta-analysis of neuroimaging studies using CVS, GVS, and auditory stimuli. We analyzed a total of 352 activation foci reported in 16 studies carried out in a total of 192 healthy participants. The results reveal that the main regions activated by CVS, GVS, or auditory stimuli were located in the Sylvian fissure, insula, retroinsular cortex, fronto-parietal operculum, superior temporal gyrus, and cingulate cortex. Conjunction analysis indicated that regions showing convergence between two stimulation methods were located in the median (short gyrus III) and posterior (long gyrus IV) insula, parietal operculum and retroinsular cortex (Ri). The only area of convergence between all three methods of stimulation was located in Ri. The data indicate that Ri, parietal operculum and posterior insula are vestibular regions where afferents converge from otoliths and semicircular canals, and may thus be involved in the processing of signals informing about body rotations, translations and tilts. Results from the meta-analysis are in agreement with electrophysiological recordings in monkeys showing main vestibular projections in the transitional zone between Ri, the insular granular field (Ig), and SII.

In recent neuroimaging studies, threshold-free cluster enhancement (TFCE) gained popularity as a sophisticated thresholding method for statistical inference. It was shown to feature higher sensitivity than the frequently used approach of controlling the cluster-level family-wise error (cFWE) and it does not require setting a cluster-forming threshold at voxel level. Here, we examined the applicability of TFCE to a widely used method for coordinate-based neuroimaging meta-analysis, Activation Likelihood Estimation (ALE), by means of large-scale simulations. We created over 200,000 artificial meta-analysis datasets by independently varying the total number of experiments included and the amount of spatial convergence across experiments. Next, we applied ALE to all datasets and compared the performance of TFCE to both voxel-level and cluster-level FWE correction approaches. All three multiple-comparison correction methods yielded valid results, with only about 5% of the significant clusters being based on spurious convergence, which corresponds to the nominal level the methods were controlling for. On average, TFCE's sensitivity was comparable to that of cFWE correction, but it was slightly worse for a subset of parameter combinations, even after TFCE parameter optimization. cFWE yielded the largest significant clusters, closely followed by TFCE, while voxel-level FWE correction yielded substantially smaller clusters, showcasing its high spatial specificity. Given that TFCE does not outperform the standard cFWE correction but is computationally much more expensive, we conclude that employing TFCE for ALE cannot be recommended to the general user.

The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal interaction data capable of describing in details the spatial interactions within a genome. These data can be used to reconstruct 3D structures of chromosomes that can be used to study DNA replication, gene regulation, genome interaction, genome folding, and genome function.

We often need to rapidly change our mind about perceptual decisions in order to account for new information and correct mistakes. One fundamental, unresolved question is whether information processed prior to a decision being made ('pre-decisional information') has any influence on the likelihood and speed with which that decision is reversed. We investigated this using a luminance discrimination task in which participants indicated which of two flickering greyscale squares was brightest. Following an initial decision, the stimuli briefly remained on screen, and participants could change their response. Using psychophysical reverse correlation, we examined how moment-to-moment fluctuations in stimulus luminance affected participants' decisions. This revealed that the strength of even the very earliest (pre-decisional) evidence was associated with the likelihood and speed of later changes of mind. To account for this effect, we propose an extended diffusion model in which an initial 'snapshot' of sensory information biases ongoing evidence accumulation.

Prostate cancer is the most common noncutaneous cancer in men in the United States. The current paradigm for screening and diagnosis is imperfect, with relatively low specificity, high cost, and high morbidity. This study aims to generate new image contrasts by learning a distribution of unique image signatures associated with prostate cancer. In total, 48 patients were prospectively recruited for this institutional review board-approved study. Patients underwent multiparametric magnetic resonance imaging 2 weeks before surgery. Postsurgical tissues were annotated by a pathologist and aligned to the in vivo imaging. Radiomic profiles were generated by linearly combining 4 image contrasts (T2, apparent diffusion coefficient [ADC] 0-1000, ADC 50-2000, and dynamic contrast-enhanced) segmented using global thresholds. The distribution of radiomic profiles in high-grade cancer, low-grade cancer, and normal tissues was recorded, and the generated probability values were applied to a naive test set. The resulting Gleason probability maps were stable regardless of training cohort, functioned independent of prostate zone, and outperformed conventional clinical imaging (area under the curve [AUC] = 0.79). Extensive overlap was seen in the most common image signatures associated with high- and low-grade cancer, indicating that low- and high-grade tumors present similarly on conventional imaging.

Forensic camera device identification addresses the scenario, where an investigator has two pieces of evidence: a digital image from an unknown camera involved in a crime, such as child pornography, and a person of interest's (POI's) camera. The investigator wants to determine whether the image was taken by the POI's camera. Small manufacturing imperfections in the photodiode cause slight variations among pixels in the camera sensor array. These spatial variations, called photo-response non-uniformity (PRNU), provide an identifying characteristic, or fingerprint, of the camera. Most work in camera device identification leverages the PRNU of the questioned image and the POI's camera to make a yes-or-no decision. As in other areas of forensics, there is a need to introduce statistical and probabilistic methods that quantify the strength of evidence in favor of the decision. Score-based likelihood ratios (SLRs) have been proposed in the forensics community to do just that. Several types of SLRs have been studied individually for camera device identification. We introduce a framework for calculating and comparing the performance of three types of SLRs - source-anchored, trace-anchored, and general match. We employ PRNU estimates as camera fingerprints and use correlation distance as a similarity score. Three types of SLRs are calculated for 48 camera devices from four image databases: ALASKA; BOSSbase; Dresden; and StegoAppDB. Experiments show that the trace-anchored SLRs perform the best of these three SLR types on the dataset and the general match SLRs perform the worst.

Brand love is a critical concept for building a relationship between brands and consumers because falling in love with a brand can lead to strong brand loyalty. Despite the importance of marketing strategies, however, the underlying neural mechanisms of brand love remain unclear. The present study used an activation likelihood estimation meta-analysis method to investigate the neural correlates of brand love and compared it with those of maternal and romantic love. In total, 47 experiments investigating brand, maternal, and romantic love were examined, and the neural systems involved for the three loves were compared and contrasted. Results revealed that the putamen and insula were commonly activated in the three loves. Moreover, activated brain regions in brand love were detected in the dorsal striatum. Activated regions for maternal love were detected in the cortical area and globus pallidus and were associated with pair bonds, empathy, and altruism. Finally, those for romantic love were detected in the hedonic, strong passionate, and intimate-related regions, such as the nucleus accumbens and ventral tegmental area. Thus, the common regions of brain activation between brand and romantic love were in the dorsal striatum. Meanwhile, no common activated regions were observed between brand and maternal love except for the regions shared among the three love types. Although brand love shared little with the two interpersonal (maternal and romantic) loves and relatively resembled aspects of romantic rather than maternal love, our results demonstrated that brand love may have intrinsically different dispositions from the two interpersonal loves.

Papillary renal cell carcinoma (PRCC) accounts for 15% of all renal cell carcinomas. The molecular mechanisms of renal papillary cell carcinoma remain unclear, and treatments for advanced disease are limited.