Miracle-dz/UniFAR-FTUs huggingface dataset:
Preliminary findings on the effect of childhood trauma on the functional connectivity of the anterior cingulate cortex subregions in major depressive disorder

Objectives Childhood trauma (CT) is a known risk factor for major depressive disorder (MDD), but the mechanisms linking CT and MDD remain unknown. The purpose of this study was to examine the influence of CT and depression diagnosis on the subregions of the anterior cingulate cortex (ACC) in MDD patients. Methods The functional connectivity (FC) of ACC subregions was evaluated in 60 first-episode, drug-naïve MDD patients (40 with moderate-to-severe and 20 with no or low CT), and 78 healthy controls (HC) (19 with moderate-to-severe and 59 with no or low CT). The correlations between the anomalous FC of ACC subregions and the severity of depressive symptoms and CT were investigated. Results Individuals with moderate-to severe CT exhibited increased FC between the caudal ACC and the middle frontal gyrus (MFG) than individuals with no or low CT, regardless of MDD diagnosis. MDD patients showed lower FC between the dorsal ACC and the superior frontal gyrus (SFG) and MFG. They also showed lower FC between the subgenual/perigenual ACC and the middle temporal gyrus (MTG) and angular gyrus (ANG) than the HCs, regardless of CT severity. The FC between the left caudal ACC and the left MFG mediated the correlation between the Childhood Trauma Questionnaire (CTQ) total score and HAMD-cognitive factor score in MDD patients. Conclusion Functional changes of caudal ACC mediated the correlation between CT and MDD. These findings contribute to our understanding of the neuroimaging mechanisms of CT in MDD.
Operationalization of a multidimensional sex/gender concept for quantitative environmental health research and implementation in the KORA study: Results of the collaborative research project INGER

Background In environmental health research, sex and gender are not yet adequately considered. There is a need to improve data collection in population-based environmental health studies by comprehensively surveying sex/gender-related aspects according to gender theoretical concepts. Thus, within the joint project INGER we developed a multidimensional sex/gender concept which we aimed to operationalize and to test the operationalization for feasibility. Methods In an iterative process, we created questionnaire modules which quantitatively captured the requirements of the INGER sex/gender concept. We deployed it in the KORA cohort (Cooperative Health Research in the Region of Augsburg, Germany) in 2019 and evaluated response and missing rates. Results The individual sex/gender self-concept was surveyed via a two-step approach that asked for sex assigned at birth and the current sex/gender identity. Additionally, we used existing tools to query internalized sex/gender roles and externalized sex/gender expressions. Adapted to the KORA population, we asked for discrimination experiences and care and household activities contributing to explain structural sex/gender relations. Further intersectionality-related social categories (e.g., socio-economic position), lifestyle and psychosocial factors were covered through data available in KORA. We could not identify appropriate tools to assess the true biological sex, sexual orientation and ethnic/cultural identity, which have yet to be developed or improved. The response-rate was 71%, the evaluation of 3,743 questionnaires showed a low missing rate. Prevalence of marginalized groups regarding sex/gender identity and definable by experiences of discrimination was very low. Conclusion We have shown how the multidimensional INGER sex/gender concept can be operationalized according to an European and North American understanding of sex/gender for use in quantitative research. The questionnaire modules proved feasible in an epidemiologic cohort study. Being a balancing act between theoretical concepts and its quantitative implementation our operationalization paves the way for an adequate consideration of sex/gender in environmental health research.
Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species

Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates—obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon—were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.
Understanding preschoolers’ word learning success in different scenarios: disambiguation meets statistical learning and eBook reading

Children’s ability to learn new words during their preschool years is crucial for further academic success. Previous research suggests that children rely on different learning mechanisms to acquire new words depending on the available context and linguistic information. To date, there is limited research integrating different paradigms to provide a cohesive view of the mechanisms and processes involved in preschool children’s word learning. We presented 4 year-old children (n = 47) with one of three different novel word-learning scenarios to test their ability to connect novel words to their correspondent referents without explicit instruction to do so. The scenarios were tested with three exposure conditions of different nature: (i) mutual exclusivity–target novel word-referent pair presented with a familiar referent, prompting fast-mapping via disambiguation, (ii) cross-situational–target novel word-referent pair presented next to an unfamiliar referent prompting statistically tracking the target pairs across trials, and (iii) eBook - target word-referent pairs presented within an audio-visual electronic storybook (eBook), prompting inferring meaning incidentally. Results show children succeed at learning the new words above chance in all three scenarios, with higher performance in eBook and mutual exclusivity than in cross-situational word learning. This illustrates children’s astounding ability to learn while coping with uncertainty and varying degrees of ambiguity, which are common in real-world situations. Findings extend our understanding of how preschoolers learn new words more or less successfully depending on specific word learning scenarios, which should be taken into account when working on vocabulary development for school readiness in the preschool years.
Urbanization may enhance tornado potential: A single case report

Tornadoes pose a risk of catastrophic economic loss and casualty in the United States. Modification of land use by urbanization alters the meteorological conditions that may impact tornado formation and intensification processes. Here we explored the simulated impact of Kansas City urbanization on the tornado potential of a supercell storm. In this studied case, we found that urbanization might enhance tornado potential by a) strengthening the low-level streamwise vorticity in the storm inflow region, thus forming stronger rotating updrafts; and b) intensifying near-surface horizontal vorticity near the boundary of the forward-flank cold pool which increases the ingestion, tilting, and stretching of streamwise horizontal vorticity into vertical vorticity. The former results from the stronger east-to-west pressure perturbation gradient due to the faster, stronger outflow boundary, and the latter is mainly a result of stronger cold fronts and a better alignment of storm-relative inflow with the horizontal vorticity vector. We emphasize that our conclusions only represent one possibility of how urbanization would affect tornado potential, and a more systematic examination is needed to achieve a more general conclusion.
Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein–DNA complexes, including the nucleosome

Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we explore, computationally, stability of a set of protein-nucleic acid complexes using fundamental thermodynamic linkage relationship. The nucleosome, as well as an essentially random selection of 20 protein complexes with DNA or RNA, are included in the analysis. An increase in intra-cellular/intra-nuclear pH destabilizes most complexes, including the nucleosome. We propose to quantify the effect by ΔΔG0.3—the change in the binding free energy due to pH increase of 0.3 units, corresponding to doubling of the H + activity; variations of pH of this amplitude can occur in living cells, including in the course of the cell cycle, and in cancer cells relative to normal ones. We suggest, based on relevant experimental findings, a threshold of biological significance of 1 2 k B T ( ∼ 0.3 k c a l / m o l ) for changes of stability of chromatin-related protein-DNA complexes: a change in the binding affinity above the threshold may have biological consequences. We find that for 70% of the examined complexes, Δ Δ G 0.3 > 1 2 k B T (for 10%, ΔΔG0.3 is between 3 and 4 k B T). Thus, small but relevant variations of intra-nuclear pH of 0.3 may have biological consequences for many protein-nucleic acid complexes. The binding affinity between the histone octamer and its DNA, which directly affects the DNA accessibility in the nucleosome, is predicted to be highly sensitive to intra-nuclear pH. A variation of 0.3 units results in ΔΔG0.3 ∼ 10k B T ( ∼ 6 k c a l / m o l ) ; for spontaneous unwrapping of 20 bp long entry/exit fragments of the nucleosomal DNA, ΔΔG0.3 = 2.2k B T; partial disassembly of the nucleosome into the tetrasome is characterized by ΔΔG0.3 = 5.2k B T. The predicted pH -induced modulations of the nucleosome stability are significant enough to suggest that they may have consequences relevant to the biological function of the nucleosome. Accessibility of the nucleosomal DNA is predicted to positively correlate with pH variations during the cell cycle; an increase in intra-cellular pH seen in cancer cells is predicted to lead to a more accessible nucleosomal DNA; a drop in pH associated with apoptosis is predicted to make nucleosomal DNA less accessible. We speculate that processes that depend on accessibility to the DNA in the nucleosomes, such as transcription or DNA replication, might become upregulated due to relatively small, but nevertheless realistic increases of intra-nuclear pH.
The relationship of trait-like compassion with epigenetic aging: The population-based prospective Young Finns Study

Introduction Helping others within and beyond the family has been related to living a healthy and long life. Compassion is a prosocial personality trait characterized by concern for another person who is suffering and the motivation to help. The current study examines whether epigenetic aging is a potential biological mechanism that explains the link between prosociality and longevity. Methods We used data from the Young Finns Study that follows six birth-cohorts from age 3–18 to 19–49. Trait-like compassion for others was measured with the Temperament and Character Inventory in the years 1997 and 2001. Epigenetic age acceleration and telomere length were measured with five DNA methylation (DNAm) indicators (DNAmAgeHorvath, IEAA_Hannum, EEAA_Hannum, DNAmPhenoAge, and DNAmTL) based on blood drawn in 2011. We controlled for sex, socioeconomic status in childhood and adulthood, and body-mass index. Results and discussion An association between higher compassion in 1997 and a less accelerated DNAmPhenoAge, which builds on previous work on phenotypic aging, approached statistical significance in a sex-adjusted model (n = 1,030; b = −0.34; p = 0.050). Compassion in 1997 predicted less accelerated epigenetic aging over and above the control variables (n = 843; b = −0.47; p = 0.016). There was no relationship between compassion in 2001 (n = 1108/910) and any of the other four studied epigenetic aging indicators. High compassion for others might indeed influence whether an individual’s biological age is lower than their chronological age. The conducted robustness checks partially support this conclusion, yet cannot rule out that there might be a broader prosocial trait behind the findings. The observed associations are interesting but should be interpreted as weak requiring replication.
Literature analysis on asparagus roots and review of its functional characterizations

Asparagus root (AR) is utilized globally as a traditional herbal medicine because it contains various bioactive compounds, such as polyphenols, flavonoids, saponins, and minerals. The composition profiles of AR are strongly affected by its botanical and geographical origins. Although minerals and heavy metals are minor constituents of AR, they play a crucial role in determining its quality and efficacy. A comprehensive classification of AR, its phytochemistry, and its pharmacology were reviewed and interpreted herein. Potentially eligible articles (in English) were identified through an electronic search of the Web of Science database (2010–2022) and Google (2001–2022). We used the primary search term “Asparagus roots” combined with the words “pharmacology,” “bioactive compounds,” “physicochemical properties,” and “health benefits” to find the relevant literature. We screened the titles, keywords, and abstracts of the publications obtained from the database. A full copy of the article was obtained for further assessment if deemed appropriate. Different asparagus species might potentially be used as herbal medicines and functional foods. Phytochemical studies have revealed the presence of various bioactive compounds as valuable secondary metabolites. The dominant class of bioactive compounds in AR is flavonoids. Furthermore, AR displayed significant pharmacological effects, such as antioxidant, antimicrobial, antiviral, anticancer, anti-inflammatory, and antidiabetic effects, as shown in animal and human studies. This review provides a valuable resource to enable a thorough assessment of the profile of Asparagus root as a functional ingredient for the pharmaceutical and food industries. In addition, it is anticipated that this review will provide information to healthcare professionals seeking alternative sources of critical bioactive compounds.
Direction splitting of φ-functions in exponential integrators for d-dimensional problems in Kronecker form

In this manuscript, we propose an efficient, practical and easy-to-implement way to approximate actions of $\varphi$-functions for matrices with $d$-dimensional Kronecker sum structure in the context of exponential integrators up to second order. The method is based on a direction splitting of the involved matrix functions, which lets us exploit the highly efficient level 3 BLAS for the actual computation of the required actions in a $\mu$-mode fashion. The approach has been successfully tested on two- and three-dimensional problems with various exponential integrators, resulting in a consistent speedup with respect to a technique designed to compute actions of $\varphi$-functions for Kronecker sums.
Pricing outside barrier options when the monitoring of the barrier starts at a hitting time

This dissertation studies the pricing of Outside barrier call options, when their activation starts at a hitting time. The pricing of Outside barrier options when their activation starts at time zero, and the pricing of standard barrier options when their activation starts at a hitting time of a pre specified barrier level, have been studied previously (see [21], [24]). The new work that this dissertation will do is to price Outside barrier call options, where they will be activated when the triggering asset crosses or hits a pre specified barrier level, and also the pricing of Outside barrier call options where they will be activated when the triggering asset crosses or hits a sequence of two pre specifed barrier levels. Closed form solutions are derived using Girsanov’s theorem and the reflection principle. Existing results are derived from the new results, and properties of the new results are illustrated numerically and discussed.
Longitudinal Changes in Value-based Learning in Middle Childhood: Distinct Contributions of Hippocampus and Striatum

The hippocampal-dependent memory system and striatal-dependent memory system modulate reinforcement learning depending on feedback timing in adults, but their contributions during development remain unclear. In a 2-year longitudinal study, 6-to-7-year-old children performed a reinforcement learning task in which they received feedback immediately or with a short delay following their response. Children’s learning was found to be sensitive to feedback timing modulations in their reaction time and inverse temperature parameter, which quantifies value-guided decision-making. They showed longitudinal improvements towards more optimal value-based learning, and their hippocampal volume showed protracted maturation. Better delayed model-derived learning covaried with larger hippocampal volume longitudinally, in line with the adult literature. In contrast, a larger striatal volume in children was associated with both better immediate and delayed model-derived learning longitudinally. These findings show, for the first time, an early hippocampal contribution to the dynamic development of reinforcement learning in middle childhood, with neurally less differentiated and more cooperative memory systems than in adults.
P roposed Definition and Typology of Brownfield Sites in Iranian Cities

ABS TRACT: The term of brownfield and its redevelopment has been considered extensively in the world urban planning literature. However, the nature of the brownfields and the differences between how they are created in countries have caused this term to be defined based on the contextual and typological conditions in each country, involving a wide range of lands. Meanwhile, despite the high importance of brownfield development in improving the quality of urban life, this issue is s till neglected in the urban planning sys tem of Iran. Therefore, this s tudy is aimed to propose the definition of brownfield sits in Iranian cities and their typology as a policy to help reconsider them in urban development plans. After presenting the adaptive criteria extracted from the relevant literature, experts in this field were interviewed to determine the main categories of this concept in the country’s cities using the grounded theory qualitative method. Then, the rules and regulations related to the categories were reviewed to finally define this concept and present its comparative typology. The findings show that in Iranian cities, the brownfield sites comprise abandoned sites or lands including activities that pollute the environment, being incompatible with authorized urban activities. According to this definition, twelve types of brownfield sites can be identified in Iranian cities, in which the activities are incompatible with urban activities and they require intervention for development, and one type includes lands with no function at present, in which development has occurred
CSGAN: Modality-Aware Trajectory Generation via Clustering-based Sequence GAN

Human mobility data is useful for various applications in urban planning, transportation, and public health, but collecting and sharing real-world trajectories can be challenging due to privacy and data quality issues. To address these problems, recent research focuses on generating synthetic trajectories, mainly using generative adversarial networks (GANs) trained by real-world trajectories. In this paper, we hypothesize that by explicitly capturing the modality of transportation (e.g., walking, biking, driving), we can generate not only more diverse and representative trajectories for different modalities but also more realistic trajectories that preserve the geographical density, trajectory, and transition level properties by capturing both cross-modality and modality-specific patterns. Towards this end, we propose a Clustering-based Sequence Generative Adversarial Network (CSGAN)1 that simultaneously clusters the trajectories based on their modalities and learns the essential properties of real-world trajectories to generate realistic and representative synthetic trajectories. To measure the effectiveness of generated trajectories, in addition to typical density and trajectory level statistics, we define several new metrics for a comprehensive evaluation, including modality distribution and transition probabilities both globally and within each modality. Our extensive experiments with real-world datasets show the superiority of our model in various metrics over state-of-the-art models.
Pose-robust face recognition via part-based sparse representation

Considering that sparse representation based classification(SRC) is sensitive to pose variation,a novel pose-robust face recognition algorithm via part-based sparse representation(PSRC) was proposed.In PSRC,an image was represented by a set of local regions first,and then the affine transformation model was used to model the pose variation.In this way,PSRC can efficiently improve the robustness of pose variation.Meanwhile,to improve the estimation accuracy of transformation parameters,PSRC got an initial estimation value by minimizing the reconstruction error of local patches.Experimental results show that PSRC can compensate for the alignment errors caused by pose variations and thus outperform most state-of-the-art methods.
TopoBERT: Exploring the topology of fine-tuned word representations

Transformer-based language models such as BERT and its variants have found widespread use in natural language processing (NLP). A common way of using these models is to fine-tune them to improve their performance on a specific task. However, it is currently unclear how the fine-tuning process affects the underlying structure of the word embeddings from these models. We present TopoBERT, a visual analytics system for interactively exploring the fine-tuning process of various transformer-based models – across multiple fine-tuning batch updates, subsequent layers of the model, and different NLP tasks – from a topological perspective. The system uses the mapper algorithm from topological data analysis (TDA) to generate a graph that approximates the shape of a model’s embedding space for an input dataset. TopoBERT enables its users (e.g. experts in NLP and linguistics) to (1) interactively explore the fine-tuning process across different model-task pairs, (2) visualize the shape of embedding spaces at multiple scales and layers, and (3) connect linguistic and contextual information about the input dataset with the topology of the embedding space. Using TopoBERT, we provide various use cases to exemplify its applications in exploring fine-tuned word embeddings. We further demonstrate the utility of TopoBERT, which enables users to generate insights about the fine-tuning process and provides support for empirical validation of these insights.