Miracle-dz/UniFAR-FTUs huggingface dataset:
Emotional Speech Perception Unfolding in Time: The Role of the Basal Ganglia

The basal ganglia (BG) have repeatedly been linked to emotional speech processing in studies involving patients with neurodegenerative and structural changes of the BG. However, the majority of previous studies did not consider that (i) emotional speech processing entails multiple processing steps, and the possibility that (ii) the BG may engage in one rather than the other of these processing steps. In the present study we investigate three different stages of emotional speech processing (emotional salience detection, meaning-related processing, and identification) in the same patient group to verify whether lesions to the BG affect these stages in a qualitatively different manner. Specifically, we explore early implicit emotional speech processing (probe verification) in an ERP experiment followed by an explicit behavioral emotional recognition task. In both experiments, participants listened to emotional sentences expressing one of four emotions (anger, fear, disgust, happiness) or neutral sentences. In line with previous evidence patients and healthy controls show differentiation of emotional and neutral sentences in the P200 component (emotional salience detection) and a following negative-going brain wave (meaning-related processing). However, the behavioral recognition (identification stage) of emotional sentences was impaired in BG patients, but not in healthy controls. The current data provide further support that the BG are involved in late, explicit rather than early emotional speech processing stages.
Deep Dictionary Learning: A PARametric NETwork Approach

Deep dictionary learning seeks multiple dictionaries at different image scales to capture complementary coherent characteristics. We propose a method for learning a hierarchy of synthesis dictionaries with an image classification goal. The dictionaries and classification parameters are trained by a classification objective, and the sparse features are extracted by reducing a reconstruction loss in each layer. The reconstruction objectives in some sense regularize the classification problem and inject source signal information in the extracted features. The performance of the proposed hierarchical method increases by adding more layers, which consequently makes this model easier to tune and adapt. The proposed algorithm furthermore shows a remarkably lower fooling rate in the presence of adversarial perturbation. The validation of the proposed approach is based on its classification performance using four benchmark datasets and is compared to a Convolutional Neural Network (CNN) of similar size.
Purine 5′,8-cyclo-2′-deoxynucleoside lesions: formation by radical stress and repair in human breast epithelial cancer cells

Abstract 5′,8-Cyclo-2′-deoxyadenosine (cdA) and 5′,8-cyclo-2′-deoxyguanosine (cdG) in their two diastereomeric forms, 5′S and 5′R, are tandem lesions produced by the attack of hydroxyl radicals to the purine moieties of DNA. Their formation has been found to challenge the cells’ repair machinery, initiating the nucleotide excision repair (NER) for restoring the genome integrity. The involvement of oxidatively induced DNA damage in carcinogenesis and the reduced capacity of some cancer cell lines to repair oxidised DNA base lesions, intrigued us to investigate the implication of these lesions in breast cancer, the most frequently occurring cancer in women. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), we measured the levels of diastereomeric cdA’s and cdG’s in estrogen receptor-alpha positive (ER-α) MCF-7 and triple negative MDA-MB-231 breast cancer cell lines before and after exposure to two different conditions: ionising radiations and hydrogen peroxide, followed by an interval period to allow DNA repair. An increase at the measured levels of all four lesions, i.e. 5′S-cdA, 5′R-cdA, 5′S-cdG and 5′R-cdG, was observed either after γ-irradiation (5 Gy dose) or hydrogen peroxide treatment (300 μM) compared to the untreated cells (control), independently from the length of the interval period for repair. For comparison reasons, we also measured the levels of 8-oxo-2′-deoxyadenosine (8-oxo-dA), a well-known oxidatively induced DNA damage lesion and base excision repair (BER) substrate. The collected data indicate that MCF-7 and MDA-MB-231 breast cancer cells are highly susceptible to radiation-induced DNA damage, being mainly defective in the repair of these lesions.
Robust inference with knockoffs

We consider the variable selection problem, which seeks to identify important variables influencing a response $Y$ out of many candidate features $X_1, \ldots, X_p$. We wish to do so while offering finite-sample guarantees about the fraction of false positives - selected variables $X_j$ that in fact have no effect on $Y$ after the other features are known. When the number of features $p$ is large (perhaps even larger than the sample size $n$), and we have no prior knowledge regarding the type of dependence between $Y$ and $X$, the model-X knockoffs framework nonetheless allows us to select a model with a guaranteed bound on the false discovery rate, as long as the distribution of the feature vector $X=(X_1,\dots,X_p)$ is exactly known. This model selection procedure operates by constructing "knockoff copies'" of each of the $p$ features, which are then used as a control group to ensure that the model selection algorithm is not choosing too many irrelevant features. In this work, we study the practical setting where the distribution of $X$ could only be estimated, rather than known exactly, and the knockoff copies of the $X_j$'s are therefore constructed somewhat incorrectly. Our results, which are free of any modeling assumption whatsoever, show that the resulting model selection procedure incurs an inflation of the false discovery rate that is proportional to our errors in estimating the distribution of each feature $X_j$ conditional on the remaining features $\{X_k:k\neq j\}$. The model-X knockoff framework is therefore robust to errors in the underlying assumptions on the distribution of $X$, making it an effective method for many practical applications, such as genome-wide association studies, where the underlying distribution on the features $X_1,\dots,X_p$ is estimated accurately but not known exactly.
Effects of Endurance and Endurance Strength Training on Body Composition and Physical Capacity in Women with Abdominal Obesity

Aims: To compare the effects of endurance training with endurance strength training on the anthropometric, body composition, physical capacity, and circulatory parameters in obese women. Methods: 44 women with abdominal obesity were randomized into groups A and B, and asked to perform endurance (A) and endurance strength training (B) for 3 months, 3 times/week, for 60 min. Dual-energy X-ray absorptiometry and Graded Exercise Test were performed before and after training. Results: Significant decreases in body mass, BMI, total body fat, total body fat mass, and waist and hip circumference were observed after both types of intervention. Marked increases in total body lean and total body fat-free mass were documented in group B. In both groups, significant increases in peak oxygen uptake, time to exhaustion, maximal work rate, and work rate at ventilatory threshold were accompanied by noticeably decreased resting heart rate, resting systolic blood pressure, and resting and exercise diastolic blood pressure. No significant differences were noticed between groups for the investigated parameters. Conclusion: Our findings demonstrate evidence for a favorable and comparable effect of 3-month endurance and endurance strength training on anthropometric parameters, body composition, physical capacity, and circulatory system function in women with abdominal obesity.
Stigma Reduction Among African American Women With HIV: UNITY Health Study

Introduction: African American women encounter disproportionately high rates of HIV-related morbidity and mortality, which is partially mediated through stigma and its effect on HIV treatment adherence. Objective: To assess the effect of the UNITY peer support workshop on HIV-related stigma among African American women living with HIV, compared with a time and attention control group. Methods: African American women living with HIV were randomized to the UNITY workshop or a breast cancer education control group. Interventions took place in HIV clinics in Chicago, IL and Birmingham, AL. Participants self-reported HIV-related stigma and social support at baseline, after workshop, and at 4 follow-up visits over 12 months. Results: Two hundred thirty-nine participants (UNITY n = 124; breast cancer education n = 115) were assessed over 1 year. Both arms experienced decreases in mean stigma scores over time. Our model estimated that allocation to UNITY was not associated with a significant difference in stigma points over time. Post hoc analysis suggested that preceding increases in perceived social support are associated with decreased HIV-related stigma in this population. Conclusions: Although UNITY did not significantly reduce HIV-related stigma in this population, our findings suggest that social support may be key to HIV-related stigma reduction.
Influence of Chloride in Reinforced Concrete

The state of knowledge regarding the action of chloride, principally calcium chloride, in reinforced concrete is reviewed, with special emphasis on its effect on the reinforcing steel. Calcium chloride's beneficial effects in ordinary reinforced concrete are enumerated, along with the precautions regarding its use in prestressed concrete and special situations. It is pointed out that the limit for chloride that has been suggested as a guide to determine the extent of repair to existing bridge decks that have been subject to repeated application of deicer salts is not a requirement that should be applied to limit the chloride content of ordinary reinforced concrete. When the amount of commercial calcium chloride is limited to 2% by weight of cement, the degree of corrosion in ordinary reinforced concrete is insignificant if the concrete is reasonable dense and there is adequate cover over the steel.
The Role of Sociocultural Influences on Symptoms of Muscle Dysmorphia and Eating Disorders in Men, and the Mediating Effects of Perfectionism

This study examined the mediating role of self-oriented and socially prescribed perfectionism in the relationship between sociocultural influences (i.e., media, peer, and teasing) and symptoms of muscle dysmorphia (MD) and eating disorders (ED). A nonclinical sample of males (N = 158, Mage = 26.94, SD = 5.50) completed measures of perfectionism, MD, body dissatisfaction, drive for thinness, and bulimia. Susceptibility to appearance-based messages from the media, their peers, and family was also measured. Analyses confirmed the partial mediating role of self-oriented perfectionism only for drive for thinness. In contrast, socially prescribed perfectionism was found to be a partial mediator between all three sociocultural variables and measures of both MD and ED; except for those between peer influence and body dissatisfaction, and teasing and bulimia symptomatology. These two relationships were fully mediated by socially prescribed perfectionism. Results suggest that vulnerability to MD and ED depend on pre-existing perfectionistic attitudes, particularly that of socially prescribed perfectionism.
Initial Standardized Uptake Value of Positron Emission Tomography Influences the Prognosis of Patients with Localized Gastric Adenocarcinoma Treated Preoperatively

Background: In patients with localized gastric adenocarcinoma (LGAC) who receive preoperative therapy, tools to predict response or prognosticate outcome before therapy are lacking. We used initial standardized uptake value (iSUV) of positron emission tomography (PET) to evaluate its association with overall survival (OS). Methods: We identified 60 patients with confirmed LGAC who were treated with preoperative chemoradiation and had a baseline PET in addition to other routine staging. Fisher's exact test and Wilcoxon's rank sum test were used to determine the association between iSUV and other variables, and the log-rank test and Cox proportional hazards model were used for survival analysis. Results: The median iSUV was 6 (range, 0-28). The presence of signet ring cells in pretreatment biopsies correlated highly with low iSUV (≤6; p = 0.0017). Patients with a high iSUV (>6) had a longer OS compared to those with a low iSUV (≤6; p = 0.0344). iSUV was not an independent predictor (p = 0.12); however, the risk of death was reduced for patients with an iSUV >6 (hazard ratio = 0.26). Conclusion: Our novel findings show that among LGAC patients treated with preoperative chemoradiation and surgery, those with a high iSUV have longer OS than patients with a low iSUV. iSUV appears to have a predictive role in patients with LGAC when treated with preoperative chemoradiation.
Searching for Subspace Trails and Truncated Differentials

Grassi et al. [Gra+16] introduced subspace trail cryptanalysis as a generalization of invariant subspaces and used it to give the first five round distinguisher for Aes. While it is a generic method, up to now it was only applied to the Aes and Prince. One problem for a broad adoption of the attack is a missing generic analysis algorithm. In this work we provide efficient and generic algorithms that allow to compute the provably best subspace trails for any substitution permutation cipher.
The Global Risk Approach Should Be Better Applied in French Hypertensive Patients: A Comparison between Simulation and Observation Studies

Background The prediction of the public health impact of a preventive strategy provides valuable support for decision-making. International guidelines for hypertension management have introduced the level of absolute cardiovascular risk in the definition of the treatment target population. The public health impact of implementing such a recommendation has not been measured. Methodology/Principal Findings We assessed the efficiency of three treatment scenarios according to historical and current versions of practice guidelines on a Realistic Virtual Population representative of the French population aged from 35 to 64 years: 1) BP≥160/95 mm Hg; 2) BP≥140/90 mm Hg and 3) BP≥140/90 mm Hg plus increased CVD risk. We compared the eligibility following the ESC guidelines with the recently observed proportion of treated amongst hypertensive individuals reported by the Etude Nationale Nutrition Santé survey. Lowering the threshold to define hypertension multiplied by 2.5 the number of eligible individuals. Applying the cardiovascular risk rule reduced this number significantly: less than 1/4 of hypertensive women under 55 years and less than 1/3 of hypertensive men below 45 years of age. This was the most efficient strategy. Compared to the simulated guidelines application, men of all ages were undertreated (between 32 and 60%), as were women over 55 years (70%). By contrast, younger women were over-treated (over 200%). Conclusion The global CVD risk approach to decide for treatment is more efficient than the simple blood pressure level. However, lack of screening rather than guideline application seems to explain the low prescription rates among hypertensive individuals in France. Multidimensional analyses required to obtain these results are possible only through databases at the individual level: realistic virtual populations should become the gold standard for assessing the impact of public health policies at the national level.
Using Parameterized Black-Box Priors to Scale Up Model-Based Policy Search for Robotics

The most data-efficient algorithms for reinforcement learning in robotics are model-based policy search algorithms, which alternate between learning a dynamical model of the robot and optimizing a policy to maximize the expected return given the model and its uncertainties. Among the few proposed approaches, the recently introduced Black-DROPS algorithm exploits a black-box optimization algorithm to achieve both high data-efficiency and good computation times when several cores are used; nevertheless, like all model-based policy search approaches, Black-DROPS does not scale to high dimensional state/action spaces. In this paper, we introduce a new model learning procedure in Black-DROPS that leverages parameterized black-box priors to (1) scale up to high-dimensional systems, and (2) be robust to large inaccuracies of the prior information. We demonstrate the effectiveness of our approach with the “pendubot” swing-up task in simulation and with a physical hexapod robot (48D state space, 18D action space) that has to walk forward as fast as possible. The results show that our new algorithm is more data-efficient than previous model-based policy search algorithms (with and without priors) and that it can allow a physical 6-legged robot to learn new gaits in only 16 to 30 seconds of interaction time.
Session-based Suggestion of Topics for Geographic Exploratory Search

Exploratory information search can challenge users in the formulation of efficacious search queries. Moreover, complex information spaces, such as those managed by Geographical Information Systems, can disorient people, making it difficult to find relevant data. In order to address these issues, we developed a session-based suggestion model that proposes concepts as a \em "you might also be interested in»» function, by taking the user»s previous queries into account. Our model can be applied to incrementally generate suggestions in interactive search. It can be used for query expansion, and in general to guide users in the exploration of possibly complex spaces of data categories. Our model is based on a concept co-occurrence graph that describes how frequently concepts are searched together in search sessions. Starting from an ontological domain representation, we generated the graph by analyzing the query log of a major search engine. Moreover, we identified clusters of ontology concepts which frequently co-occur in the sessions of the log via community detection on the graph. The evaluation of our model provided satisfactory accuracy results.
Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling

Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ∼0.31%/MY (CI: 0.27–0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings represent an important contribution to the systematics of Salmonidae, and provide a useful tool for addressing questions related to fundamental and applied evolutionary issues.
The completed eight chloroplast genomes of tomato from Solanum genus

Abstract In this study, we fully assembled eight tomato chloroplast (cp) genomes using next-generation sequencing data. It will provide valuable information for phylogenetic and cp genetic engineering studies of Solanum genus. The total genome size varied from 155,443 to 155,561 bp in length, containing a pair of inverted repeats (IRs) of 25,612–25,639 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 85,857–85,911 bp and 18,362–18,387 bp in size, respectively. The overall GC contents of the chloroplast genome were 37.84–37.88%. The same set of 112 unique genes was annotated from eight cp genomes, including 78 protein coding genes, 30 tRNA genes, and four rRNA genes. Among these, 17 are duplicated in the inverted repeat regions, 15 genes contained one intron, and three genes (rps12, clpP, and ycf3) comprising two introns.
Global Patterns of Guild Composition and Functional Diversity of Spiders

The objectives of this work are: (1) to define spider guilds for all extant families worldwide; (2) test if guilds defined at family level are good surrogates of species guilds; (3) compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4) compare the taxonomic and functional diversity of spider assemblages and; (5) relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1) sensing, (2) sheet, (3) space, and (4) orb web weavers; (5) specialists; (6) ambush, (7) ground, and (8) other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also influenced by altitude and habitat structure.