Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial organization of the mouse retina at single cell resolution

The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. We performed spatial transcriptomic profiling of over 100,000 cells from the mouse retina, uncovering the spatial distribution of all major retina cell types with over 100 cell subtypes. Our data revealed that the retina is organized in a laminar structure at the major cell type and subgroup level, both of which has strong correlation with the birth order of the cell. In contrast, overall random dispersion of cells within sub-laminar layers indicates that retinal mosaics are driven by dendritic field patterning rather than neuron soma placement. Through the integration of single cell transcriptomic and spatial data, we have generated the first comprehensive spatial single cell reference atlas of the mouse retina, a resource to the community and an essential step toward gaining a comprehensive understanding of the mechanism of retinal function. Graphical Abstract
A scoping review on the use of consumer-grade EEG devices for research

Background Commercial electroencephalography (EEG) devices have become increasingly available over the last decade. These devices have been used in a wide variety of fields ranging from engineering to cognitive neuroscience. Purpose The aim of this study was to chart peer-review articles that used consumer-grade EEG devices to collect neural data. We provide an overview of the research conducted with these relatively more affordable and user-friendly devices. We also inform future research by exploring the current and potential scope of consumer-grade EEG. Methods We followed a five-stage methodological framework for a scoping review that included a systematic search using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines. We searched the following online databases: PsycINFO, MEDLINE, Embase, Web of Science, and IEEE Xplore. We charted study data according to application (BCI, experimental research, validation, signal processing, and clinical) and location of use as indexed by the first author’s country. Results We identified 916 studies that used data recorded with consumer-grade EEG: 531 were reported in journal articles and 385 in conference papers. Emotiv devices were used most, followed by the NeuroSky MindWave, OpenBCI, interaXon Muse, and MyndPlay Mindband. The most common usage was for brain-computer interfaces, followed by experimental research, signal processing, validation, and clinical purposes. Conclusions Consumer-grade EEG is a useful tool for neuroscientific research and will likely continue to be used well into the future. Our study provides a comprehensive review of their application, as well as future directions for researchers who plan to use these devices.
Mathematical modeling of mechanosensing and contact-dependent motility coordination in Myxococcus xanthus

Sensing and responding to mechanical cues in the environment are important for the survival and propagation of bacteria. A ‘social’ bacterium, Myxococcus xanthus, which exhibits periodic cell reversals, modulates its reversal frequency in response to environmental mechanical cues, such as substrate stiffness and cell-cell contact. In M. xanthus populations, the cell-cell contact-dependent reversal control is particularly important for formation of complex multicellular patterns and structures during the cooperative ‘social’ behaviors. Here we hypothesize that the gliding motility machinery of M. xanthus can sense the environmental mechanical cues during force generation and modulate the timing and frequency of cell reversal through signaling the cell’s reversal control pathway. To examine our hypothesis, we extend an existing mathematical model for periodic polarity switching (which mediates periodic cell reversal) in M. xanthus, and incorporate the experimentally suggested (i) intracellular dynamics of the gliding motors and (ii) interactions between the gliding motors and reversal regulators. The model results suggest the proper mode of interaction between the gliding motors and reversal regulators that can generate the observed increase of cell reversal frequency on stiffer substrates. Furthermore, the selected model predicts a cell reversal response to cell-cell contact, which is sufficient for generating the rippling wave, an important multicellular pattern in M. xanthus populations. Our model highlights a potential role of the gliding machinery of M. xanthus as a ‘mechanosensor’ that transduces mechanical cues into a reversal control signal.
Robust Online Multiband Drift Estimation in Electrophysiology Data

High-density electrophysiology probes have opened new possibilities for systems neuroscience in human and non-human animals, but probe motion (or drift) while recording poses a challenge for downstream analyses, particularly in human recordings. Here, we improve on the state of the art for tracking this drift with an algorithm termed DREDge (Decentralized Registration of Electrophysiology Data) with four major contributions. First, we extend previous decentralized methods to exploit multiband information, leveraging the local field potential (LFP), in addition to spikes detected from the action potentials (AP). Second, we show that the LFP-based approach enables registration at sub-second temporal resolution. Third, we introduce an efficient online motion tracking algorithm, allowing the method to scale up to longer and higher spatial resolution recordings, which could facilitate real-time applications. Finally, we improve the robustness of the approach by accounting for the nonstationarities that occur in real data and by automating parameter selection. Together, these advances enable fully automated scalable registration of challenging datasets from both humans and mice.
Servant leadership and job satisfaction: The mediating role of trust and leader-member exchange

Objective The study aimed to examine the role of trust mediation and leader-member exchange in the influence of servant leadership on job satisfaction. Background Research on the relationship between servant leadership and academic job satisfaction is rare. The study of servant leadership in Christian higher education is dominated by non-research (conceptual), literature review, and church ministry, instrument development, verification, and validation, quantitative (pre- and post-test), quantitative (descriptive), and qualitative studies. Thus, there have been no studies that test and measure complex variables simultaneously in one model that includes servant leadership, trust (job-related outcomes + mediator), leader-member exchange (behavioral outcome), and job satisfaction (well-being + outcome) in the context of Christian higher education in Indonesia. Servant leadership still needs to be done in work-related outcomes such as trust variables. Research on academic job satisfaction in non-European and non-Western contexts is still dominant in Palestine. Finally, the placement of trust as a mediation variable needs to be more consistent because trust also has a role as a predictor of servant leadership. Method This study used quantitative methods with a sample of 160 lecturers from 26 Christian higher education in Indonesia. This study used the partial least square (PLS-SEM) approach to verify the proposed hypothesis. Results The results showed that servant leadership has a significant positive effect on job satisfaction and trust, and LMX mediate the influence of servant leadership on job satisfaction. Finally, trust and LMX are complementary mediation effects of servant leadership on job satisfaction. Conclusion Servant leadership increases trust, LMX and job satisfaction. Trust and LMX increase job satisfaction. Trust and LMX have a mediating role in the effect of servant leadership on job satisfaction. Implications Rectors/chairmen who engage in high-level interactions with lecturers will influence trust, reduce losses, and maximize gains in their interactional relationships. In addition, based on the theory of leader-member exchange, high-quality, trustworthy, and satisfactory leader-member exchange relationships positively affect the personal growth, work attitudes, and performance of lecturers. The Private Higher Education Organizing Body (BPPTS) needs to prepare for leadership regeneration by preparing future service leaders through training that directly supports the improvement of servant leadership behavior. This is important because servant leadership behavior becomes essential to increase trust, LMX and lecturer job satisfaction and achieve Christian higher education goals. Finally, Power distances, short-term orientation cultures, and paternalistic are not found to be obstacles to servant leadership practices in Indonesian Christian higher education.
Social prescribing of nature therapy for adults with mental illness living in the community: A scoping review of peer-reviewed international evidence

Social prescribing of nature therapy “green social prescribing” facilitates access to local nature-based activities that improve biopsychosocial wellbeing outcomes, are affordable, accessible, and can be adapted to context. These are becoming increasingly popular and gray literature is emerging, however, peer-reviewed scientific evidence is exiguous. This scoping review aimed to identify and critique peer-reviewed evidence for green social prescribing interventions and develop recommendations for research and clinical practice. Included studies were published in peer-reviewed journals in English on/after 1 January 2000. Participants were community-living adults with mental illness; Intervention was any green social prescribing program; Comparator was not restricted/required; Outcomes were any biopsychosocial measures; and any/all Study Designs were included. Twelve databases were searched on 15 October 2022; these were Academic Search Premier, APA PsycArticles, APA PsycINFO, CINAHL, Cochrane Library, Google Scholar, JSTOR, ProQuest, PubMed, Science Direct, Scopus, and Web of Science. The Mixed Methods Appraisal Tool was used to assess quality. Seven publications describing 6 unique studies (5 UK, 1 Australia) were identified including 3 mixed-methods, 2 qualitative, and 1 RCT. Participants included 334 adults (45% female, aged 35–70 years); sample sizes ranged from 9 to 164. All studies showed improvements in biopsychosocial wellbeing, and participants from most studies (n = 5) reported increased connection to the earth and intention to further access nature. Participant demographics and diagnoses were poorly reported, and intervention activities and assessments varied considerably. However, MMAT scores were good overall suggesting these studies may reliably demonstrate intervention outcomes. We conclude that socially prescribed nature therapy can improve biopsychosocial wellbeing and is a potentially important intervention for mental illness. Recommendations for research and clinical practice are provided.
Spatial opinion dynamics incorporating both positive and negative influence in small-world networks

When we consider tipping points of political and social opinions in groups, we often rely on a physics-based opinion dynamics approach. Despite the many studies on simple models, studies on more realistic situations have yet to be done. In this paper, we extend the basic model of opinion dynamics in two ways. The first extension incorporates negative influence between individuals. The second arranges individuals in a small-world network and fixes them in neighborhoods to consider their relationships. Our results show that a consensus tends to result with a higher positive trust ratio in the network, a denser network, and a milder degree of trust between individuals. In a real society, the development of consensus opinions depends on frequent communication, reliable people, and mild opinions. Moreover, we explore the conditions for merging the majority with a minority of individuals who are strongly connected. Our dense city model shows that the opinions of two parties connecting in dense interactions will gradually attract each other, and when a certain threshold is exceeded, those opinions will be integrated at once like a phase transition.
Microbiome-based solutions to address new and existing threats to food security, nutrition, health and agrifood systems' sustainability

In addition to challenges like climate change and biodiversity loss, the sustainability and resilience of agrifood systems worldwide are currently challenged by new threats, such as the COVID-19 pandemic and the Ukraine war. Furthermore, the resilience and sustainability of our agrifood systems need to be enhanced in ways that simultaneously increase agricultural production, decrease post-harvest food losses and food waste, protect the climate, environment and health, and preserve biodiversity. The precarious situation of agrifood systems is also illustrated by the fact that overall, around 3 billion people worldwide still do not have regular access to a healthy diet. This results in various forms of malnutrition, as well as increasing number of people suffering from overweight and obesity, and diet-related, non-communicable diseases (NCDs) around the world. Findings from microbiome research have shown that the human gut microbiome plays a key role in nutrition and diet-related diseases and thus human health. Furthermore, the microbiome of soils, plants, and animals play an equally important role in environmental health and agricultural production. Upcoming, microbiome-based solutions hold great potential for more resilient, sustainable, and productive agrifood systems and open avenues toward preventive health management. Microbiome-based solutions will also be key to make better use of natural resources and increase the resilience of agrifood systems to future emerging and already-known crises. To realize the promises of microbiome science and innovation, there is a need to invest in enhancing the role of microbiomes in agrifood systems in a holistic One Health approach and to accelerate knowledge translation and implementation.
Flos Puerariae-Semen Hoveniae medicinal pair extract ameliorates DSS-induced inflammatory bowel disease through regulating MAPK signaling and modulating gut microbiota composition

Background: Inflammatory bowel disease (IBD) is a global gastrointestinal disease characterized by relapsing and remitting inflammatory conditions. Flos Puerariae (the flower of Pueraria lobata [Willd.] Ohwi and P. thomsonii Benth.) and Hovenia dulcis Thunb. (Rhamnaceae) are traditional Chinese medicines. This medicinal pair has been used to treat various diseases due to its excellent anti-oxidant and anti-inflammatory activity. However, the effects of extracts from these plants on dextran sulfate sodium (DSS)-induced colitis have not been investigated; further study is needed to improve the understanding of their mechanisms of action and potential applications. Methods: The chemical constitution of extracts from Flos Puerariae and Semen Hoveniae (PHE) was analyzed using UPLC-LTQ-Orbitrap-MS/MS. The protective effects of PHE on mice with DSS-induced colitis were evaluated through assessment of body weight loss, disease activity index (DAI) score, colon length shortening, and pathological changes. The levels of inflammatory cytokines were determined by ELISA and RT-qPCR. Biomarkers of oxidative stress (ROS, CAT, SOD, MDA, and T-AOC) were analyzed using biochemical kits. The expression of MAPK proteins was determined by Western blotting analysis. Gut microbiota were analyzed via 16S rRNA sequencing. Results: Chemical composition analysis indicated that PHE contains various bioactive compounds, including puerarin, kakkalide, tectoridin, and genistin. The findings from this study suggest that PHE could effectively modulate histopathological score, inflammatory cell infiltration, and inflammatory factor secretion. Notably, PHE ameliorated oxidative stress by inhibiting activation of the MAPK pathway, leading to decreased inflammatory mediators and restored antioxidant enzyme activity. Furthermore, PHE treatment regulated the composition of the gut microbiota by increasing the abundance of benign bacteria, such as Akkermansia, and reducing the abundance of harmful bacteria, such as Proteobacteria. Conclusion: The findings from this study demonstrate the mechanism underlying the amelioration of DSS-induced intestinal oxidative stress by PHE and its positive impact on the restoration of the composition of gut microbiota.
Application of feedback control to stomatal optimisation in a global land surface model

Accurate representations of stomatal conductance are required to predict the effects of climate change on terrestrial ecosystems. Stomatal optimisation theory, the idea that plants have evolved to maximise carbon gain under certain constraints, such as minimising water loss or preventing hydraulic damage, is a powerful approach to representing stomatal behaviour that bypasses the need to represent complex physiological processes. However, while their ability to replicate observed stomatal responses is promising, optimisation models often present practical problems for those trying to simulate the land surface. In particular, when realistic models of photosynthesis and more complex cost functions are used, closed-form solutions for the optimal stomatal conductance are often very difficult to find. As a result, implementing stomatal optimisation in land surface models currently relies either on simplifying approximations, that allow closed-form solutions to be found, or on numerical iteration which can be computationally expensive. Here we propose an alternative approach, using a method motivated by control theory that is computationally efficient and does not require simplifying approximations to be made to the underlying optimisation. Stomatal conductance is treated as the control variable in a simple closed-loop system and we use the Newton-Raphson method to track the time-varying maximum of the objective function. We compare the method to both numerical iteration and a semi-analytical approach by applying the methods to the SOX stomatal optimisation model at multiple sites across the Amazon rainforest. The feedback approach is able to more accurately replicate the results found by numerical iteration than the semi-analytical approach while maintaining improved computational efficiency.
Case report: Fractional brain tumor burden magnetic resonance mapping to assess response to pulsed low-dose-rate radiotherapy in newly-diagnosed glioblastoma

Background Pulsed low-dose-rate radiotherapy (pLDR) is a commonly used reirradiation technique for recurrent glioma, but its upfront use with temozolomide (TMZ) following primary resection of glioblastoma is currently under investigation. Because standard magnetic resonance imaging (MRI) has limitations in differentiating treatment effect from tumor progression in such applications, perfusion-weighted MRI (PWI) can be used to create fractional tumor burden (FTB) maps to spatially distinguish active tumor from treatment-related effect. Methods We performed PWI prior to re-resection in four patients with glioblastoma who had undergone upfront pLDR concurrent with TMZ who had radiographic suspicion for tumor progression at a median of 3 months (0-5 months or 0-143 days) post-pLDR. The pathologic diagnosis was compared to retrospectively-generated FTB maps. Results The median patient age was 55.5 years (50-60 years). All were male with IDH-wild type (n=4) and O6-methylguanine-DNA methyltransferase (MGMT) hypermethylated (n=1) molecular markers. Pathologic diagnosis revealed treatment effect (n=2), a mixture of viable tumor and treatment effect (n=1), or viable tumor (n=1). In 3 of 4 cases, FTB maps were indicative of lesion volumes being comprised predominantly of treatment effect with enhancing tumor volumes comprised of a median of 6.8% vascular tumor (6.4-16.4%). Conclusion This case series provides insight into the radiographic response to upfront pLDR and TMZ and the role for FTB mapping to distinguish tumor progression from treatment effect prior to redo-surgery and within 20 weeks post-radiation.
Social independence evaluation index for Japanese patients with childhood-onset chronic diseases

Introduction This study established an independent evaluation index for patients with childhood-onset chronic diseases in Japan. Methods From November to December 2020, three Delphi rounds were conducted. Thirty-nine participants completed at least one survey. We asked them about targets of social independence for 10 types of activities (education/labor/finance/acquisition of necessities/housing/transportation/leisure/social relationship/intimate relationships/sexuality). The Delphi technique was to be repeated until a consensus of over 80% of participants was reached. Results The targets chosen for measuring independence in patients with childhood-onset chronic diseases were as follows: “Graduation from high school,” “Labor for livelihood (including temporary turnover),” “Financially independent (including temporary turnover, excluding students),” “Buy or rent a house and buy the daily necessities and get the public services you need to live,” “Do housework alone,” “Plan alone and use transportation to get around,” “Participate in play/recreation/leisure activities on own initiative,” “Engage in relationships with other people outside of a limited environment (home, school, office, hospital, etc.),” “Create and maintain intimate or romantic relationships between individuals (couples, lovers, sexual partners),” and “Use or know how to use contraceptives and how to prevent sexually transmitted diseases. ” Conclusions We established an independent evaluation index for patients with childhood-onset chronic diseases in Japan through a three-round Delphi process. The assessment of social independence using our independent evaluation index may help plan for and provide appropriate support and assistance to these patients.
A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods

Affinity maturation (AM) of B cells through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal lineages of antibody-secreting b cells that have evolved from a common naïve B cell. Advances in high-throughput sequencing have enabled deep scans of B cell receptor repertoires, paving the way for reconstructing clonal trees. However, it is not clear if clonal trees, which capture microevolutionary time scales, can be reconstructed using traditional phylogenetic reconstruction methods with adequate accuracy. In fact, several clonal tree reconstruction methods have been developed to fix supposed shortcomings of phylogenetic methods. Nevertheless, no consensus has been reached regarding the relative accuracy of these methods, partially because evaluation is challenging. Benchmarking the performance of existing methods and developing better methods would both benefit from realistic models of clonal lineage evolution specifically designed for emulating B cell evolution. In this paper, we propose a model for modeling B cell clonal lineage evolution and use this model to benchmark several existing clonal tree reconstruction methods. Our model, designed to be extensible, has several features: by evolving the clonal tree and sequences simultaneously, it allows modeling selective pressure due to changes in affinity binding; it enables scalable simulations of large numbers of cells; it enables several rounds of infection by an evolving pathogen; and, it models building of memory. In addition, we also suggest a set of metrics for comparing clonal trees and measuring their properties. Our results show that while maximum likelihood phylogenetic reconstruction methods can fail to capture key features of clonal tree expansion if applied naively, a simple post-processing of their results, where short branches are contracted, leads to inferences that are better than alternative methods.