Miracle-dz/UniFAR-FTUs huggingface dataset:
How Does the Fusion of Sensory Information From Audition and Vision Impact Collective Behavior?

The present study investigates how combined information from audition and vision impacts group-level behavior. We consider a modification to the original Vicsek model that allows individuals to use auditory and visual sensing modalities to gather information from neighbors in order to update their heading directions. Moreover, in this model, the information from visual and auditory cues can be weighed differently. In a simulation study, we examine the sensitivity of the emergent group-level behavior to the weights that are assigned to each sense modality in this weighted composite model. Our findings suggest combining sensory cues may play an important role in the collective behavior and results from the composite model indicate that the group-level features from pure audition predominate.
Shedding Light on Primary Donors in Photosynthetic Reaction Centers

Chlorophylls (Chl)s exist in a variety of flavors and are ubiquitous in both the energy and electron transfer processes of photosynthesis. The functions they perform often occur on the ultrafast (fs–ns) time scale and until recently, these have been difficult to measure in real time. Further, the complexity of the binding pockets and the resulting protein-matrix effects that alter the respective electronic properties have rendered theoretical modeling of these states difficult. Recent advances in experimental methodology, computational modeling, and emergence of new reaction center (RC) structures have renewed interest in these processes and allowed researchers to elucidate previously ambiguous functions of Chls and related pheophytins. This is complemented by a wealth of experimental data obtained from decades of prior research. Studying the electronic properties of Chl molecules has advanced our understanding of both the nature of the primary charge separation and subsequent electron transfer processes of RCs. In this review, we examine the structures of primary electron donors in Type I and Type II RCs in relation to the vast body of spectroscopic research that has been performed on them to date. Further, we present density functional theory calculations on each oxidized primary donor to study both their electronic properties and our ability to model experimental spectroscopic data. This allows us to directly compare the electronic properties of hetero- and homodimeric RCs.
“Eventually, I Admitted, ‘I Cannot Do This Alone’”: Exploring Experiences of Suicidality and Help-Seeking Drivers Among Australian Men

While research has explored the intersection between masculinities and men’s experiences of suicidality, comparatively little attention has been paid to the stories surrounding suicidal men’s decision to seek help. The ways in which men experiencing suicidal thoughts and behaviors embody masculinities alongside their enlistment of mental health services remains largely unknown. The present study explored 262 Australian men’s stories surrounding the impetus for help-seeking for suicidal thoughts and behaviors. The sample comprised men ranging in age from 17 to 74 years (M = 40.99; SD = 15.92 years), with most participants residing in a metropolitan area (55.3%), employed full time (43.1%), non-indigenous (95.4%) and heterosexual (73.7%). Participants elaborated on their reasons for help-seeking via an open-text qualitative survey, delivered as part of a larger study exploring help-seeking experiences of Australian men. Thematic analysis of responses generated four themes highlighting the diversity of experience across men, with some highlighting impacts of emasculating early trauma(s) on their suicidality, while others reflected an impulsiveness tied to situational stressors that fractured their masculine identity (e.g., relationship breakdown; job loss). Many men had epiphanies as they reached the limits of their self-reliance and came to terms with their need for help. As their suicidality was witnessed by—and began to impact—those around them, the sight of their previously masked pain by others often facilitated their help-seeking journey. The present findings underscore the complex and multifactorial role of masculinities in men’s suicidality and their paths to help-seeking. Important inroads for future public mental health promotion efforts are discussed, in terms of leveraging self-reliant and caring masculinities in helping men to develop healthy coping in the context of suicidality.
Be Green to Be Innovative: The Role of Government Subsidies

Corporate environmental investment has long been recognized as a non-market strategy that helps secure both economic and social benefits. However, we know much less about how environmental investment affects corporate innovation. We argue that investment in environmental protection is an important source of institutional legitimacy for firms to secure government resources, thus providing financial support for corporate innovation activities. Using a sample of Chinese industrial firms, we find that firms investing more in environmental protection can receive more government subsidies and then have better innovation performance. This study emphasizes the mechanism of government resources, which enriches our understanding of the effect of environmental investment on corporate innovation.
XBP-1s Promotes B Cell Pathogenicity in Chronic GVHD by Restraining the Activity of Regulated IRE-1α-Dependent Decay

Allogeneic hematopoietic cell transplantation (allo-HCT) is an effective therapeutic procedure to treat hematological malignancies. However, the benefit of allo-HCT is limited by a major complication, chronic graft-versus-host disease (cGVHD). Since transmembrane and secretory proteins are generated and modified in the endoplasmic reticulum (ER), the ER stress response is of great importance to secretory cells including B cells. By using conditional knock-out (KO) of XBP-1, IRE-1α or both specifically on B cells, we demonstrated that the IRE-1α/XBP-1 pathway, one of the major ER stress response mediators, plays a critical role in B cell pathogenicity on the induction of cGVHD in murine models of allo-HCT. Endoribonuclease activity of IRE-1α activates XBP-1 signaling by converting unspliced XBP-1 (XBP-1u) mRNA into spliced XBP-1 (XBP-1s) mRNA but also cleaves other ER-associated mRNAs through regulated IRE-1α-dependent decay (RIDD). Further, ablation of XBP-1s production leads to unleashed activation of RIDD. Therefore, we hypothesized that RIDD plays an important role in B cells during cGVHD development. In this study, we found that the reduced pathogenicity of XBP-1 deficient B cells in cGVHD was reversed by RIDD restriction in IRE-1α kinase domain KO mice. Restraining RIDD activity per se in B cells resulted in an increased severity of cGVHD. Besides, inhibition of RIDD activity compromised B cell differentiation and led to dysregulated expression of MHC II and costimulatory molecules such as CD86, CD40, and ICOSL in B cells. Furthermore, restraining the RIDD activity without affecting XBP-1 splicing increased B cell ability to induce cGVHD after allo-HCT. These results suggest that RIDD is an important mediator for reducing cGVHD pathogenesis through targeting XBP-1s.
STING Signaling and Sterile Inflammation

Innate immunity is regulated by a broad set of evolutionary conserved receptors to finely probe the local environment and maintain host integrity. Besides pathogen recognition through conserved motifs, several of these receptors also sense aberrant or misplaced self-molecules as a sign of perturbed homeostasis. Among them, self-nucleic acid sensing by the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) pathway alerts on the presence of both exogenous and endogenous DNA in the cytoplasm. We review recent literature demonstrating that self-nucleic acid detection through the STING pathway is central to numerous processes, from cell physiology to sterile injury, auto-immunity and cancer. We address the role of STING in autoimmune diseases linked to dysfunctional DNAse or related to mutations in DNA sensing pathways. We expose the role of the cGAS/STING pathway in inflammatory diseases, neurodegenerative conditions and cancer. Connections between STING in various cell processes including autophagy and cell death are developed. Finally, we review proposed mechanisms to explain the sources of cytoplasmic DNA.
Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage Structure

Chromatin accessibility, as measured by ATACseq, varies between hematopoietic cell types in different lineages of the hematopoietic differentiation tree, e.g. T cells vs. B cells, but methods that associate variation in chromatin accessibility to the lineage structure of the differentiation tree are lacking. Using an ATACseq dataset recently published by the ImmGen consortium, we construct associations between chromatin accessibility and hematopoietic cell types using a novel co-clustering approach that accounts for the structure of the hematopoietic, differentiation tree. Under a model in which all loci and cell types within a co-cluster have a shared accessibility state, we show that roughly 80% of cell type associated accessibility variation can be captured through 12 cell type clusters and 20 genomic locus clusters, with the cell type clusters reflecting coherent components of the differentiation tree. Using publicly available ChIPseq datasets, we show that our clustering reflects transcription factor binding patterns with implications for regulation across cell types. We show that traditional methods such as hierarchical and kmeans clusterings lead to cell type clusters that are more dispersed on the tree than our tree-based algorithm. We provide a python package, chromcocluster, that implements the algorithms presented.
Murine Susceptibility to Leishmania amazonensis Infection Is Influenced by Arginase-1 and Macrophages at the Lesion Site

Cutaneous leishmaniasis is a zoonotic infectious disease broadly distributed worldwide, causing a range of diseases with clinical outcomes ranging from self-healing infections to chronic disfiguring disease. The effective immune response to this infection is yet to be more comprehensively understood and is fundamental for developing drugs and vaccines. Thus, we used experimental models of susceptibility (BALB/c) and partial resistance (C57BL/6) to Leishmania amazonensis infection to investigate the local profile of mediators involved in the development of cutaneous leishmaniasis. We found worse disease outcome in BALB/c mice than in C57BL/6 mice, with almost 15 times higher parasitic load, ulcerated lesion formation, and higher levels of IL-6 in infected paws. In contrast, C57BL/6 presented higher levels of IFN-γ and superoxide anion ( • O 2 − ) after 11 weeks of infection and no lesion ulcerations. A peak of local macrophages appeared after 24 h of infection in both of the studied mice strains, followed by another increase after 240 h, detected only in C57BL/6 mice. Regarding M1 and M2 macrophage phenotype markers [iNOS, MHC-II, CD206, and arginase-1 (Arg-1)], we found a pronounced increase in Arg-1 levels in BALB/c after 11 weeks of infection, whereas C57BL/6 showed an initial predomination of markers from both profiles, followed by an M2 predominance, coinciding with the second peak of macrophage infiltration, 240 h after the infection. Greater deposition of type III collagen and lesion resolution was also observed in C57BL/6 mice. The adoptive transfer of macrophages from C57BL/6 to infected BALB/c at the 11th week showed a reduction in both edema and the number of parasites at the lesion site, in addition to lower levels of Arg-1. Thus, C57BL/6 mice have a more effective response against L. amazonensis, based on a balance between inflammation and tissue repair, while BALB/c mice have an excessive Arg-1 production at late infection. The worst evolution seems to be influenced by recruitment of Arg-1 related macrophages, since the adoptive transfer of macrophages from C57BL/6 mice to BALB/c resulted in better outcomes, with lower levels of Arg-1.
Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Zebrafish have been found to be a premier model organism in biological and regeneration research. However, the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here, we utilized Microwell-seq to analyze more than 250,000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single-cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single-cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall, our single-cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research.
A Conserved Structural Role for the Walker-A Lysine in P-Loop Containing Kinases

Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved “catalytic” lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg2+•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by the catalytic lysine, stabilize a state in SKs that deviates significantly from one that is necessary for the optimal coordination of Mg2+•ATP. This structural role of the Walker-A lysine is a general feature in SKs and is found to be present in members that encode a Walker-B sequence characteristic of the family (Coxiella burnetii SK), and in those that do not (Mycobacterium tuberculosis SK). Thus, the structural role of the Walker-A lysine in stabilizing an inactive state, distinct from its catalytic function, is conserved between two distantly related P-loop containing kinase families, the SKs and the BY-kinases. The universal conservation of this element, and of the key characteristics of its associated interaction partners within the Walker motifs of P-loop containing enzymes, suggests that this structural role of the Walker-A lysine is perhaps a widely deployed regulatory mechanism within this ancient family.
Validating the General Extended Technology Acceptance Model for E-Learning: Evidence From an Online English as a Foreign Language Course Amid COVID-19

The present study validated the general extended technology acceptance model for e-learning (GETAMEL) with the survey data from the English as a foreign language (EFL) online class during the novel coronavirus lockdown period. A total of 678 undergraduates participated in the survey. Structural equation modeling was employed to analyze the data. The results showed that the influence of perceived usefulness of students on their intentional behavior to use the online learning system was not mediated by their attitude, indicating a very limited role of attitude toward technology in the model. Enjoyment and self-efficacy had no significant effects on the internal constructs, raising theoretical concerns on the applicability of this general model into specific contexts. In addition, we found that experience might be a moderator rather than an antecedent of the internal constructs in the model.
Sex-Differences in the Oxygenation Levels of Intercostal and Vastus Lateralis Muscles During Incremental Exercise

This study aimed to examine sex differences in oxygen saturation in respiratory (SmO2-m.intercostales) and locomotor muscles (SmO2-m.vastus lateralis) while performing physical exercise. Twenty-five (12 women) healthy and physically active participants were evaluated during an incremental test with a cycle ergometer, while ventilatory variables [lung ventilation (V.E), tidal volume (Vt), and respiratory rate (RR)] were acquired through the breath-by-breath method. SmO2 was acquired using the MOXY® devices on the m.intercostales and m.vastus lateralis. A two-way ANOVA (sex × time) indicated that women showed a greater significant decrease of SmO2-m.intercostales, and men showed a greater significant decrease of SmO2-m.vastus lateralis. Additionally, women reached a higher level of ΔSmO2-m.intercostales normalized to V.E (L⋅min–1) (p < 0.001), whereas men had a higher level of ΔSmO2-m.vastus lateralis normalized to peak workload-to-weight (watts⋅kg–1, PtW) (p = 0.049), as confirmed by Student’s t-test. During an incremental physical exercise, women experienced a greater cost of breathing, reflected by greater deoxygenation of the respiratory muscles, whereas men had a higher peripheral load, indicated by greater deoxygenation of the locomotor muscles.
Rare Co-Occurrence of Visual Snow in a Female Carrier With RPGRORF15-Associated Retinal Disorder

X-linked retinitis pigmentosa (XLRP), a rare form of retinitis pigmentosa (RP), is predominantly caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. Affected males often present with severe phenotypes and early disease onset. In contrast, female carriers are usually asymptomatic or show stationary phenotypes. Herein, we reported an 8-year-old female carrier, a daughter of a confirmed RP father with RPGR mutation, with an early onset of progressive cone-rod pattern retinal dystrophy. Additionally, the carrier experienced visual snow-like symptom as long as she recalled. Ophthalmological examination showed the reduction of visual acuity and attenuation of photoreceptor functions since the age of 5 years. Further analysis revealed a heterozygous pathogenic variant of the RPGR gene and a random X-inactivation pattern. Although she harboured an identical RPGR variant as the father, there were phenotypic intrafamilial variations. The information on the variety of genotypic and phenotypic presentations in XLRP carriers is essential for further diagnosis, management, and monitoring of these cases, including the design of future gene therapy trials.
A Novel Self-Assembled Gel for Gastric Endoscopic Submucosal Dissection-Induced Ulcer: A Preclinical Study in a Porcine Model

Endoscopic submucosal dissection (ESD) is a routine procedure for the management of early gastrointestinal neoplasia, but it results in large ulcers. This study aims to examine the feasibility and effectiveness of a newly developed self-assembled gel on the ulcer healing process after ESD. Sixteen 2.0-cm (diameter) gastric ulcers were created by ESD in five pigs. All ulcers were randomized: control group (n = 7, routine ulcer management) and gel-treated group (n = 9). The gel was applied to cover the whole ulcer bed through the endoscope immediately after ESD. The feasibility of this endoscopic treatment modality was macroscopically accessed by endoscopy. The effectiveness was evaluated based on the ulcer area and histology changes at 14 days after ESD. The gel-treated group showed higher healing activity compared with the control ulcers on day 14 after ESD. The percentage of healing was higher for the gel-treated ulcers than in control ones (96.2 ± 2.2% vs. 91.9 ± 4.5%, p = 0.035). The extent of the new epithelium covering the ulcer was greater in the gel group than in controls. One delayed overt bleeding occurred in the control group (14.3%). This novel gel might promote the speed of ulcer healing after ESD, leading to higher epithelium formation.
Toward Zero Hunger Through Coupled Ecological Sanitation-Agriculture Systems

Ecological sanitation (EcoSan) systems capture and sanitize human excreta and generate organic nutrient resources that can support more sustainable nutrient management in agricultural ecosystems. An emerging EcoSan system that is implemented in Haiti and several other contexts globally couples container-based household toilets with aerobic, thermophilic composting. This closed loop sanitation system generates organic nutrient resources that can be used as part of an ecological approach to soil nutrient management and thus has the potential to contribute to Sustainable Development Goals 2 (zero hunger), 6 (clean water and sanitation for all), and 13 (climate change solutions). However, the role of organic nutrient resources derived from human excreta in food production is poorly studied. We conducted a greenhouse experiment comparing the impact of feces-derived compost on crop production, soil nutrient cycling, and nutrient losses with two amendments produced from wastewater treatment (pelletized biosolids and biofertilizer), urea, and an unfertilized control. Excreta-derived amendments increased crop yields 2.5 times more than urea, but had differing carry-over effects. After a one-time application of compost, crop production remained elevated throughout all six crop cycles. In contrast, the carry-over of crop response lasted two and four crop cycles for biosolids and biofertilizer, respectively, and was absent for urea. Soil carbon concentration in the compost amended soils increased linearly through time from 2.0 to 2.5%, an effect not seen with other treatments. Soil nitrous oxide emissions factors ranged from 0.3% (compost) to 4.6% (biosolids), while nitrogen leaching losses were lowest for biosolids and highest for urea. These results indicate that excreta-derived compost provides plant available nutrients, while improving soil health through the addition of soil organic carbon. It also improved biogeochemical functions, indicating the potential of excreta-derived compost to close nutrient loops if implemented at larger scales. If captured and safely treated through EcoSan, human feces produced in Haiti can meet up to 13, 22, and 11% of major crop needs of nitrogen, phosphorus, and potassium, respectively.