Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain structural correlates of alexithymia in patients with major depressive disorder

Background Alexithymia is a risk factor for major depressive disorder (MDD) and has been associated with diminished treatment response. Neuroimaging studies have revealed structural aberrations of the anterior cingulate cortex and the fusiform gyrus in healthy controls with high levels of alexithymia. The present study tried to corroborate and extend these results to patients with MDD compared with healthy controls. Methods We investigated the relationship between alexithymia, depression and grey matter volume in 63 patients with MDD (mean age ± standard deviation = 42.43 yr ± 11.91; 33 female) and 46 healthy controls (45.35 yr ± 8.37; 22 female). We assessed alexithymia using the Toronto Alexithymia Scale. We conducted an alexithymia × group analysis of covariance; we used a region-of-interest approach, including the fusiform gyrus and anterior cingulate cortex, and conducted whole brain analysis using voxelbased morphometry. Results Our analysis revealed a significant alexithymia × group interaction in the fusiform gyrus (left, pFWE = 0.031; right, pFWE = 0.010). Higher alexithymia scores were associated with decreased grey matter volume in patients with MDD (pFWE = 0.009), but with increased grey matter volume of the fusiform gyrus in healthy controls (pFWE = 0.044). We found no significant main effects in the region-of-interest analysis. Limitations Owing to the naturalistic nature of our study, patients with MDD and healthy controls differed significantly in their alexithymia scores. Conclusion Our results showed the fusiform gyrus as a correlate of alexithymia. We also found differences related to alexithymia between patients with MDD and healthy controls in the fusiform gyrus. Our study encourages research related to the transition from risk to MDD in people with alexithymia.
Epigenetic clocks and allostatic load reveal potential sex-specific drivers of biological ageing.

Allostatic Load (AL) and epigenetic clocks both attempt to characterise the accelerated ageing of biological systems, but at present it is unclear whether these measures are complementary or distinct. This study examines the cross-sectional association of AL with Epigenetic Age Acceleration (EAA) in a sub-sample of 490 community dwelling older-adults participating in The Irish Longitudinal study on Aging (TILDA). A battery of 14 biomarkers representing the activity of 4 different physiological systems: immunological, cardiovascular, metabolic, renal, was used to construct the AL score. DNA methylation age was computed according to the algorithms described by Horvath, Hannum and Levine allowing for estimation of whether an individual is experiencing accelerated or decelerated ageing. Horvath, Hannum and Levine EAA correlated 0.05, 0.03, and 0.21 with AL respectively. Disaggregation by sex revealed that AL was more strongly associated with EAA in men compared with women as assessed using Horvath's clock. Metabolic dysregulation was a strong driver of EAA in men as assessed using Horvath and Levine's clock, while metabolic and cardiovascular dysregulation were associated with EAA in women using Levine's clock. Results indicate that AL and the epigenetic clocks are measuring different age-related variance and implicate sex-specific drivers of biological ageing.
Towards a Technique for Modeling New Forms of Collaborative Work Practices - The Facilitation Process Model 2.0

Collaboration Engineering (CE) is an approach for the design and deployment of repeatable collaborative work practices that can be executed by practitioners themselves without the ongoing support of external collaboration professionals. A key design activity in CE concerns modeling current and future collaborative work practices. CE researchers and practitioners have used the Facilitation Process Model (FPM) technique. However, this modeling technique suffers from a number of shortcomings to model contemporary collaborative work practices. We use a design science approach to identify the main challenges with the original FPM technique, derive requirements and design a revised modeling technique that is based on the current technique enriched by BPMN 2.0 elements. This paper contributes to the CE literature by offering a revised FPM technique that assists CE-designers to capture new forms of collaborative work practices.
Privacy concerns could derail Facebook data-sharing plan.

A novel collaboration designed to give researchers access to information on Facebook9s 2 billion users could unravel over delays in preparing the data for release. A dozen research teams studying whether the ubiquitous social platform is helping sway elections and undermine political institutions around the world has been promised the website addresses that Facebook users have publicly shared, some characteristics of those URLs, and aggregated information about the sharers, including their age, gender, location, and political leanings. But that research, funded by a consortium of foundations, is not yet underway, and next week the funders are expected to suspend their support because many of the data have not been released. Facebook decided to adopt a rigorous statistical technique known as differential privacy to ensure that individual users cannot be identified. But the company is still figuring out how to apply differential privacy to all the data, and it9s not clear when—or whether—the scientists will ever have access to them.
A Provenance Task Abstraction Framework

Visual analytics tools integrate provenance recording to externalize analytic processes or user insights. Provenance can be captured on varying levels of detail, and in turn activities can be characterized from different granularities. However, current approaches do not support inferring activities that can only be characterized across multiple levels of provenance. We propose a task abstraction framework that consists of a three stage approach, composed of 1) initializing a provenance task hierarchy, 2) parsing the provenance hierarchy by using an abstraction mapping mechanism, and 3) leveraging the task hierarchy in an analytical tool. Furthermore, we identify implications to accommodate iterative refinement, context, variability, and uncertainty during all stages of the framework. We describe a use case which exemplifies our abstraction framework, demonstrating how context can influence the provenance hierarchy to support analysis. The article concludes with an agenda, raising and discussing challenges that need to be considered for successfully implementing such a framework.
Managing hemolyzed samples in clinical laboratories

Abstract Hemolysis is conventionally defined as membrane disruption of red blood cells and other blood cells that is accompanied by subsequent release of intracellular components into the serum or plasma. It accounts for over 60% of blood sample rejections in the laboratory and is the most common preanalytical error in laboratory medicine. Hemolysis can occur both in vivo and in vitro. Intravascular hemolysis (in vivo) is always associated with an underlying pathological condition or disease, and thus careful steps should always be taken by the laboratory to exclude in vivo hemolysis with confidence. In vitro hemolysis, on the other hand, is highly preventable. It may occur at all stages of the preanalytical phase (i.e. sample collection, transport, handling and storage), and may lead to clinically relevant, yet spurious, changes in patient results by interfering with laboratory measurements. Hemolysis interference is exerted through several mechanisms: (1) spectrophotometric interference, (2) release of intracellular components, (3) sample dilution and (4) chemical interference. The degree of interference observed depends on the level of hemolysis and also on the assay methodology. Recent evidence shows that preanalytical practices related to detection and management of hemolyzed samples are highly heterogeneous and need to be standardized. The Working Group for Preanalytical Phase (WG-PRE) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) has published many recommendations for facilitating standardization and improvement of this important preanalytical issue. Some key EFLM WG-PRE publications related to hemolysis involve: (i) a call for more transparency and some practical recommendations for improving the harmonization of the automatic assessment of serum indices and their clinical usefulness, specifically the hemolysis index (H-index), (ii) recommendations on how to manage local quality assurance of serum or plasma hemolysis/icterus/lipemia-indices (HIL-indices) and (iii) recommendations on how to detect and manage hemolyzed samples in clinical chemistry testing. In this review we provide a comprehensive overview of hemolysis, including its causes and effects on clinical laboratory assays. Furthermore, we list and discuss the most recent recommendations aimed at managing hemolyzed samples in everyday practice. Given the high prevalence of hemolyzed blood samples, the associated costs, the great heterogeneity in how hemolysis is handled across healthcare settings, countries and continents, and increasing patient cross-border mobility, standardization and quality improvement processes aimed at combatting this important preanalytical problem are clearly warranted.
The Association Between Type of Sexual Assault and Post-Assault Alcohol Misuse Is Moderated by Avoidance Among Recipients of a Sexual Assault Medical Forensic Examination.

OBJECTIVE The purpose of this study was to examine the association between the type of sexual assault (intoxicated vs. non-intoxicated) and post-assault avoidance on post-assault alcohol misuse among people who experienced a recent sexual assault. METHOD The sample included 72 adults aged 18-58 who completed a follow-up phone screen within 30 days of completing a sexual assault medical forensic examination. Participants reported demographics, prior sexual assault, if they were intoxicated from alcohol or other drugs during the sexual assault that preceded receipt of a sexual assault medical forensic examination, post-assault avoidance symptoms, and post-assault alcohol misuse. RESULTS Post-assault alcohol misuse was higher among participants with intoxicated (vs. non-intoxicated) sexual assault, prior sexual assault (vs. none), and who identified as White. There was a significant interaction between the type of sexual assault and avoidance symptoms on post-assault alcohol misuse. There was a significant association between avoidance symptoms and alcohol misuse (b = 0.82, p = .003) among participants who experienced a non-intoxicated sexual assault, but not among those who reported intoxication during the recent sexual assault (b = -0.33, p = .468). CONCLUSIONS Intoxicated sexual assault and post-assault avoidance may be influential factors contributing to post-assault alcohol misuse among people who are recently sexually assaulted. Interventions targeting post-sexual assault alcohol misuse should be tailored based on the type of recent assault and post-assault avoidance.
Method and system for encoding pronunciation prefix trees

Kind of linearly encoded pronunciation prefix tree computer system. Wherein each node represents a phoneme, each leaf node having a probability value associated with the word of the node, the system generates a tree node dictionary phoneme identification, according to the child nodes of each non-leaf node descendants the maximum value of the probability of the leaf nodes of the child node to sort, which probability value is provided for each non-leaf node according to the probability of its child nodes, each node coefficient values ​​set to their probability value of its parent node probability point value. Finally, the computer system generates an encoded pronunciation entry for each leaf node.
Histological examination of explanted tissue-engineered bovine pericardium following heart valve repair.

OBJECTIVES Our goal was to present histopathological findings of human explants of a tissue-engineered bovine pericardium CardioCel (Admedus Regen Pty Ltd, Malaga, WA, Australia) used for heart valve repair in patients with congenital and acquired heart valve disease. METHODS Sixty patients underwent heart valve repair from May 2014 to November 2018 using CardioCel as a substitute for valve tissue. We identified 9 cases in which the CardioCel patch was explanted following valve repair and available for histomorphological analyses. CardioCel explants were evaluated histologically using haematoxylin and oeosin, Elastica van Gieson and immunohistochemical stains. RESULTS The indications for explantation were related to the CardioCel patch in 6 patients. Median time between the implantation and explantation was 242 (range 3-1247) days. We demonstrated a characteristic remodelling pattern with superficial coating of the tissue-engineered bovine pericardium by granulation tissue composed of histiocytes, few lymphocytes and fibrin. We had 2 cases with a multifocal nodular disruption, fragmentation and sclerosis of the decellularized collagen matrix with focal calcification after 795 and 1247 days in situ. CONCLUSIONS Our data suggest that the tissue-engineered CardioCel patch is initially tolerated in the valvular position in the majority of patients. However, we also experienced graft failures that showed degeneration with fragmentation of the collagen matrix and even 2 cases with focal calcification evident from the histopathological analysis. Further analyses of mid- and long-term performance are mandatory.
Phenylbutyrate facilitates homeostasis of non-resolving inflammatory macrophages

Non-resolving inflammatory monocytes/macrophages are critically involved in the pathogenesis of chronic inflammatory diseases. However, mechanisms of macrophage polarization are not well understood, thus hindering the development of effective strategies to promote inflammation resolution. In this study, we report that macrophages polarized by subclinical super-low dose LPS preferentially expressed pro-inflammatory mediators such as ccl2 (which encodes the protein monocyte chemo attractant protein-1) with reduced expression of anti-inflammatory/homeostatic mediators such as slc40a1 (which encodes the protein ferroportin-1). We observed significantly elevated levels of the autophagy-associated and pro-inflammatory protein p62 in polarized macrophages, closely correlated with the inflammatory activation of ccl2 gene expression. In contrast, we noted a significant increase of ubiquitinated/inactive nuclear-erythroid-related factor 2 (NRF2), consistent with reduced slc40a1 gene expression in polarized macrophages. Addition of the homeostatic restorative agent phenylbutyrate (4-PBA) effectively reduced cellular levels of p62 as well as ccl2 gene induction by super-low dose LPS. On the other hand, application of 4-PBA also blocked the accumulation of ubiquitinated NRF2 and restored anti-inflammatory slc40a1 gene expression in macrophages. Together, our study provides novel insights with regard to macrophage polarization and reveals 4-PBA as a promising molecule in restoring macrophage homeostasis.
A Novel Approach on Visual Question Answering by Parameter Prediction using Faster Region Based Convolutional Neural Network

Visual Question Answering (VQA) is a stimulating process in the field of Natural Language Processing (NLP) and Computer Vision (CV). In this process machine can find an answer to a natural language question which is related to an image. Question can be open-ended or multiple choice. Datasets of VQA contain mainly three components; questions, images and answers. Researchers overcome the VQA problem with deep learning based architecture that jointly combines both of two networks i.e. Convolution Neural Network (CNN) for visual (image) representation and Recurrent Neural Network (RNN) with Long Short Time Memory (LSTM) for textual (question) representation and trained the combined network end to end to generate the answer. Those models are able to answer the common and simple questions that are directly related to the image’s content. But different types of questions need different level of understanding to produce correct answers. To solve this problem, we use faster Region based-CNN (R-CNN) for extracting image features with an extra fully connected layer whose weights are dynamically obtained by LSTMs cell according to the question. We claim in this paper that a single R-CNN architecture can solve the problems related to VQA by modifying weights in the parameter prediction layer. Authors trained the network end to end by Stochastic Gradient Descent (SGD) using pretrained faster R-CNN and LSTM and tested it on benchmark datasets of VQA.
No evidence of Gremlin1-mediated activation of VEGFR2 signaling in endothelial cells

Canonical Gremlin1 (GREM1) signaling involves binding to and sequestering bone morphogenetic proteins (BMPs) in the extracellular matrix, preventing the activation of cognate BMP receptor. Exquisite temporospatial control of the GREM1-BMP interaction is required during development, and perturbation of this balance leads to abnormal limb formation and defective kidney development. In addition to inhibition of BMP signaling, several other noncanonical signaling modalities of GREM1 have been postulated. Some literature reports have suggested that GREM1 can bind to and activate vascular endothelial growth factor receptor-2 (VEGFR2) in endothelial cells, human kidney epithelial cells, and others. These reports suggest that the GREM1 → VEGFR2 signaling can drive angiogenesis both in vitro and in vivo. We report here that, despite exhaustive attempts, we did not observe GREM1 activation of VEGFR2 in any of the cell lines reported by the above-mentioned studies. Incubation of endothelial colony–forming cells (ECFCs) or human umbilical vein endothelial cells (HUVECs) with recombinant VEGF triggered a robust increase in VEGFR2 tyrosine phosphorylation. In contrast, no VEGFR2 phosphorylation was detected when cells were incubated with recombinant GREM1 over a range of time points and concentrations. We also show that GREM1 does not interfere with VEGF-mediated VEGFR2 activation, suggesting that GREM1 does not bind with any great affinity to VEGFR2. Measurements of ECFC barrier integrity revealed that VEGF induces barrier function disruption, but recombinant human GREM1 had no effect in this assay. We believe that these results provide an important clarification of the potential interaction between GREM1 and VEGFR2 in mammalian cells.
Omics Forecasting: Predictive Calculations Permit the Rapid Interpretation of High-Resolution Mass Spectral Data from Complex Mixtures.

For some complex mixtures, chromatographic techniques are insufficient to separate the large numbers of compounds present. In addition, these mixtures often contain compounds with similar or identical molecular masses and shared fragmentation transitions. Advancements in mass spectrometry have provided more and more detailed molecular profiles with significant increases in resolution. This has led to a capacity to distinguish a very large number of compounds in complex mixtures, providing overwhelming data sets. The approach of calculating molecular formulae from a mass list has become more and more problematic as the number of signals has increased exponentially, to the point that it has become impossible to manually interpret the thousands of mass signals. The current approach is to calculate a list of possible formulae that fall within a specific mass error of the observed signal. Then, one must look for possible structures that can be derived from each entry on the list of formulae. However, an alternative approach is to anticipate the possible structures of a particular set of compounds, such as red wine pigments, and then compare the ion signals against a predicted list. To that end, starting with known wine pigment types, we have generated a set of expected wine pigment variants based on known derivatives of condensed tannin oligomers, anthocyanins, and fermentation products. After accounting for the ability to distinguish compounds by mass spectrometry, over 1 million results were generated consisting of known and anticipated wine pigments. A comparison with a small sample of wine phenolic fractions show a large number of matches, suggesting that this approach may be helpful. Further analysis of mass spectral fragmentation is needed to resolve isomers.
A New Recall of Alcohol Marketing Scale for Youth: Measurement Properties and Associations With Youth Drinking Status.

OBJECTIVE Adolescents are exposed to alcohol marketing through traditional advertising and through newer digital media channels. Cumulative marketing exposure across channels is of concern but has been insufficiently studied. This study explores the measurement of alcohol marketing exposure across channels and whether cumulative recalled exposure is independently associated with underage drinking. METHOD Two hundred two New England adolescents (ages 12-17 years) were recruited from a general pediatrics clinic and completed an online survey. Recall of alcohol marketing across channels (e.g., Internet, magazines) was assessed, along with drinking behavior and relevant covariates (i.e., demographics, parental/peer drinking, smoking status, sensation seeking, Internet use, social media use, television use, and parental Internet monitoring). Confirmatory factor analysis was used to establish a latent construct of alcohol marketing exposure recall. Logistic regression tested associations between alcohol marketing recall and adolescent drinking, with covariates controlled for. RESULTS Adolescents reported recall of alcohol marketing across all marketing channels. Alcohol marketing recall items were significantly correlated, with α = . 83. The latent measurement model of alcohol marketing recall provided excellent fit to the data, χ2(17, n = 202) = 27.402, p = . 052; root mean square error of approximation (.000-.092) = . 055; Tucker-Lewis Index = . 960; comparative fit index = . 976; standardized root mean square residual = . 037). Adjusted cross-sectional logistic regression analyses demonstrated that the latent alcohol marketing recall construct was significantly associated with underage drinking (adjusted odds ratio = 4.08, 95% CI [1.15, 14.46]) when relevant covariates were accounted for. CONCLUSIONS The final measurement model provided support for construct validity of a novel alcohol marketing recall construct assessing cumulative cross-channel marketing exposure. Adolescent recall of alcohol marketing across channels was significantly associated with underage drinking, while associated factors such as peer/parental drinking were accounted for.