Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Aberrant link between empathy and social attribution style in borderline personality disorder

In social interactions, we often need to quickly infer why other people do what they do. More often than not, we infer that behavior is a result of personality rather than circumstances. It is unclear how the tendency itself may contribute to psychopathology and interpersonal dysfunction. Borderline personality disorder (BPD) is characterized by severe interpersonal dysfunction. Here, we nvestigated if this dysfunction is related to the tendency to over-attribute behaviors to personality traits. Healthy controls and patients with BPD judged positive and negative behaviors presented within a situational constraint during functional magnetic resonance imaging. Before the experiment, we measured trait levels of empathy, paranoia, and need for cognition. Behaviorally, we found that empathy levels predicted the tendency to attribute behavior to traits in healthy controls, whereas in patients with BPD this relationship was significantly weakened. Whole brain analysis of group-by-empathy interaction revealed that when participants judged the behavior during the attribution phase, several brain regions implicated in mentalizing distinguished patients from controls: In healthy controls, neural activity scaled negatively with empathy, but this relationship was reversed in BPD patients. Due to the cross-sectional study design we cannot establish a causal link between empathy and social ttributions. These findings indicate that the self-reported tendency to feel for others is related to the tendency to integrate situational information beyond personality. In BPD patients, by contrast, the association between empathy and attribution was significantly weaker, rendering empathy less informative in predicting the overall attribution style

Aberrant link between empathy and social attribution style in borderline personality disorder

In social interactions, we often need to quickly infer why other people do what they do. More often than not, we infer that behavior is a result of personality rather than circumstances. It is unclear how the tendency itself may contribute to psychopathology and interpersonal dysfunction. Borderline personality disorder (BPD) is characterized by severe interpersonal dysfunction. Here, we investigated if this dysfunction is related to the tendency to over-attribute behaviors to personality traits. Healthy controls and patients with BPD judged positive and negative behaviors presented within a situational constraint during functional magnetic resonance imaging. Before the experiment, we measured trait levels of empathy, paranoia, and need for cognition. Behaviorally, we found that empathy levels predicted the tendency to attribute behavior to traits in healthy controls, whereas in patients with BPD this relationship was significantly weakened. Whole brain analysis of group-by-empathy interaction revealed that when participants judged the behavior during the attribution phase, several brain regions implicated in mentalizing distinguished patients from controls: In healthy controls, neural activity scaled negatively with empathy, but this relationship was reversed in BPD patients. Due to the cross-sectional study design we cannot establish a causal link between empathy and social attributions. These findings indicate that the self-reported tendency to feel for others is related to the tendency to integrate situational information beyond personality. In BPD patients, by contrast, the association between empathy and attribution was significantly weaker, rendering empathy less informative in predicting the overall attribution style

Stressor controllability modulates fear extinction in humans

Traumatic events are proposed to play a role in the development of anxiety disorders, however not all individuals exposed to extreme stress experience a pathological increase in fear. Recent studies in animal models suggest that the degree to which one is able to control an aversive experience is a critical factor determining its behavioral consequences. In this study, we examined whether stressor controllability modulates subsequent conditioned fear expression in humans. Participants were randomly assigned to an escapable stressor condition, a yoked inescapable stressor condition, or a control condition involving no stress exposure. One week later, all participants underwent fear conditioning, fear extinction, and a test of extinction retrieval the following day. Participants exposed to inescapable stress showed impaired fear extinction learning and increased fear expression the following day. In contrast, escapable stress improved fear extinction and prevented the spontaneous recovery of fear. Consistent with the bidirectional controllability effects previously reported in animal models, these results suggest that one's degree of control over aversive experiences may be an important factor influencing the development of psychological resilience or vulnerability in humans.Psycholog

The brain activation-based sexual image classifier (BASIC): a sensitive and specific fMRI activity pattern for sexual image processing

Previous studies suggest there is a complex relationship between sexual and general affective stimulus processing, which varies across individuals and situations. We examined whether sexual and general affective processing can be distinguished at the brain level. In addition, we explored to what degree possible distinctions are generalizable across individuals and different types of sexual stimuli, and whether they are limited to the engagement of lower-level processes, such as the detection of visual features. Data on sexual images, nonsexual positive and negative images, and neutral images from Wehrum et al. (2013) (N = 100) were reanalyzed using multivariate support vector machine models to create the brain activation-based sexual image classifier (BASIC) model. This model was tested for sensitivity, specificity, and generalizability in cross-validation (N = 100) and an independent test cohort (N = 18; Kragel et al. 2019). The BASIC model showed highly accurate performance (94-100%) in classifying sexual versus neutral or nonsexual affective images in both datasets with forced choice tests. Virtual lesions and tests of individual large-scale networks (e.g., visual or attention networks) show that individual networks are neither necessary nor sufficient to classify sexual versus nonsexual stimulus processing. Thus, responses to sexual images are distributed across brain systems

2015 Brainhack Proceedings

Table of contents I1 Introduction to the 2015 Brainhack Proceedings R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller A1 Distributed collaboration: the case for the enhancement of Brainspell’s interface AmanPreet Badhwar, David Kennedy, Jean-Baptiste Poline, Roberto Toro A2 Advancing open science through NiData Ben Cipollini, Ariel Rokem A3 Integrating the Brain Imaging Data Structure (BIDS) standard into C-PAC Daniel Clark, Krzysztof J. Gorgolewski, R. Cameron Craddock A4 Optimized implementations of voxel-wise degree centrality and local functional connectivity density mapping in AFNI R. Cameron Craddock, Daniel J. Clark A5 LORIS: DICOM anonymizer Samir Das, Cécile Madjar, Ayan Sengupta, Zia Mohades A6 Automatic extraction of academic collaborations in neuroimaging Sebastien Dery A7 NiftyView: a zero-footprint web application for viewing DICOM and NIfTI files Weiran Deng A8 Human Connectome Project Minimal Preprocessing Pipelines to Nipype Eric Earl, Damion V. Demeter, Kate Mills, Glad Mihai, Luka Ruzic, Nick Ketz, Andrew Reineberg, Marianne C. Reddan, Anne-Lise Goddings, Javier Gonzalez-Castillo, Krzysztof J. Gorgolewski A9 Generating music with resting-state fMRI data Caroline Froehlich, Gil Dekel, Daniel S. Margulies, R. Cameron Craddock A10 Highly comparable time-series analysis in Nitime Ben D. Fulcher A11 Nipype interfaces in CBRAIN Tristan Glatard, Samir Das, Reza Adalat, Natacha Beck, Rémi Bernard, Najmeh Khalili-Mahani, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans A12 DueCredit: automated collection of citations for software, methods, and data Yaroslav O. Halchenko, Matteo Visconti di Oleggio Castello A13 Open source low-cost device to register dog’s heart rate and tail movement Raúl Hernández-Pérez, Edgar A. Morales, Laura V. Cuaya A14 Calculating the Laterality Index Using FSL for Stroke Neuroimaging Data Kaori L. Ito, Sook-Lei Liew A15 Wrapping FreeSurfer 6 for use in high-performance computing environments Hans J. Johnson A16 Facilitating big data meta-analyses for clinical neuroimaging through ENIGMA wrapper scripts Erik Kan, Julia Anglin, Michael Borich, Neda Jahanshad, Paul Thompson, Sook-Lei Liew A17 A cortical surface-based geodesic distance package for Python Daniel S Margulies, Marcel Falkiewicz, Julia M Huntenburg A18 Sharing data in the cloud David O’Connor, Daniel J. Clark, Michael P. Milham, R. Cameron Craddock A19 Detecting task-based fMRI compliance using plan abandonment techniques Ramon Fraga Pereira, Anibal Sólon Heinsfeld, Alexandre Rosa Franco, Augusto Buchweitz, Felipe Meneguzzi A20 Self-organization and brain function Jörg P. Pfannmöller, Rickson Mesquita, Luis C.T. Herrera, Daniela Dentico A21 The Neuroimaging Data Model (NIDM) API Vanessa Sochat, B Nolan Nichols A22 NeuroView: a customizable browser-base utility Anibal Sólon Heinsfeld, Alexandre Rosa Franco, Augusto Buchweitz, Felipe Meneguzzi A23 DIPY: Brain tissue classification Julio E. Villalon-Reina, Eleftherios Garyfallidi

Prophylactic biological mesh reinforcement versus standard closure of stoma site (ROCSS): a multicentre, randomised controlled trial

Background: Closure of an abdominal stoma, a common elective operation, is associated with frequent complications; one of the commonest and impactful is incisional hernia formation. We aimed to investigate whether biological mesh (collagen tissue matrix) can safely reduce the incidence of incisional hernias at the stoma closure site. Methods: In this randomised controlled trial (ROCSS) done in 37 hospitals across three European countries (35 UK, one Denmark, one Netherlands), patients aged 18 years or older undergoing elective ileostomy or colostomy closure were randomly assigned using a computer-based algorithm in a 1:1 ratio to either biological mesh reinforcement or closure with sutures alone (control). Training in the novel technique was standardised across hospitals. Patients and outcome assessors were masked to treatment allocation. The primary outcome measure was occurrence of clinically detectable hernia 2 years after randomisation (intention to treat). A sample size of 790 patients was required to identify a 40% reduction (25% to 15%), with 90% power (15% drop-out rate). This study is registered with ClinicalTrials.gov, NCT02238964. Findings: Between Nov 28, 2012, and Nov 11, 2015, of 1286 screened patients, 790 were randomly assigned. 394 (50%) patients were randomly assigned to mesh closure and 396 (50%) to standard closure. In the mesh group, 373 (95%) of 394 patients successfully received mesh and in the control group, three patients received mesh. The clinically detectable hernia rate, the primary outcome, at 2 years was 12% (39 of 323) in the mesh group and 20% (64 of 327) in the control group (adjusted relative risk [RR] 0·62, 95% CI 0·43–0·90; p=0·012). In 455 patients for whom 1 year postoperative CT scans were available, there was a lower radiologically defined hernia rate in mesh versus control groups (20 [9%] of 229 vs 47 [21%] of 226, adjusted RR 0·42, 95% CI 0·26–0·69; p<0·001). There was also a reduction in symptomatic hernia (16%, 52 of 329 vs 19%, 64 of 331; adjusted relative risk 0·83, 0·60–1·16; p=0·29) and surgical reintervention (12%, 42 of 344 vs 16%, 54 of 346: adjusted relative risk 0·78, 0·54–1·13; p=0·19) at 2 years, but this result did not reach statistical significance. No significant differences were seen in wound infection rate, seroma rate, quality of life, pain scores, or serious adverse events. Interpretation: Reinforcement of the abdominal wall with a biological mesh at the time of stoma closure reduced clinically detectable incisional hernia within 24 months of surgery and with an acceptable safety profile. The results of this study support the use of biological mesh in stoma closure site reinforcement to reduce the early formation of incisional hernias. Funding: National Institute for Health Research Research for Patient Benefit and Allergan