Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking Nutraceutical Soybean Composition Relative to Protein and Oil

The aim of this study was to explore relationships between protein, oil, and seed weight with seed nutraceutical composition, focused on total isoflavone (TI) and total tocopherol (TT) contents across genotypic and environmental combinations in soybean. We conducted a synthesis-analysis of peer-reviewed published field studies reporting TI, TT, protein, oil, and seed weight (n = 1,908). The main outcomes from this synthesis-analysis were: (i) relationship of TI-to-protein concentration was positive, though for the upper boundary, TI decreases with increases in protein; (ii) relationship of TT-to-oil concentration was positive, but inconsistent when oil was expressed in mg per seed; and (iii) as seed weight increased, TI accumulation was less than proportional relative to protein concentration and TT decreased more proportional relative to oil concentration. Association between nutraceuticals and protein, oil, and seed weight for soybean reported in the present study can be used as a foundational knowledge for soybean breeding programs interested on predicting and selecting enhanced meal isoflavone and/or oil tocopherol contents.
Modeling the Multidimensional Predictors of Multisite Musculoskeletal Pain Across Adulthood—A Generalized Estimating Equations Approach

Background: Multisite pain is commonly chronic and often lacks its initial role as a potential tissue damage signal. Chronic pain among working-age individuals is a risk for disability and imposes a major burden on health care systems and society. As effective treatments for chronic pain are largely lacking, better identification of the factors associated with pain over working years is needed. Methods: Members of the Northern Finland Birth Cohort 1966 participated in data collection at the ages of 31 (n = 4,028) and 46 (n = 3,429). Using these two time points, we performed a multivariable analysis of the association of socioeconomic, occupational, psychological and lifestyle factors (i.e., low education, living alone, low household income, unemployment, occupational physical exposures [hard physical labor, leaning forward, back twisting, constant moving, lifting loads of ≥ 1 kg], physical inactivity, regular smoking, regular drinking, overweight, and psychiatric symptoms) with the number of musculoskeletal pain sites (i.e., upper extremity, lower extremity, lower back, and the neck-shoulder region; totalling 0–4 pain sites). The data were analyzed using generalized estimating equations. Results: At the age of 31, multisite pain was reported by 72.5% of men and 78.6% of women. At the age of 46, the prevalence of multisite pain was 75.7% among men and 82.7% among women. Among men, the number of pain sites was positively associated with age (rate ratio 1.05, 95% confidence interval 1.01–1.08), low household income (1.05, 1.01–1.08), unemployment (1.13, 1.06–1.19), any occupational exposure (1.17, 1.12–1.22), regular smoking (1.06, 1.02–1.11), and psychiatric symptoms (1.21, 1.17–1.26). Among women, the number of pain sites was positively associated with age (1.06, 1.04–1.10), unemployment (1.10, 1.05–1.15), any occupational exposure (1.10, 1.06–1.13), regular smoking (1.06, 1.02–1.10), overweight (1.08, 1.05–1.11), and psychiatric symptoms (1.19, 1.15–1.22); living alone was negatively associated with the number of pain sites (0.95, 0.91–0.99). Conclusion: Of the studied predictors, psychiatric symptoms, occupational physical exposures and unemployment were most strongly associated with multisite pain among both sexes. The results of this study deepen the understanding of the underlying factors of and comorbidities behind multisite pain, and help develop pain relief and rehabilitation strategies for working-age individuals with multisite pain.
Negative Emotion Differentiation Attenuates the Within-Person Indirect Effect of Daily Stress on Nightly Sleep Quality Through Calmness

The ability to differentiate between negative emotional states [negative emotion differentiation (NED)] has been conceptualized as a trait that facilitates effective emotion regulation and buffers stress reactivity. In the present research, we investigated the role of NED in within-person processes of daily affect regulation and coping during times of stress (the first COVID-19-related pandemic lockdown in April 2020). Using intensive longitudinal data, we analyzed whether daily stress had an indirect effect on sleep quality through calmness in the evening, and we tested whether NED moderated this within-person indirect effect by buffering the link between daily stress and calmness in the evening. A non-representative community sample (n = 313, 15–82 years old) participated in a 21-day ambulatory assessment with twice-daily surveys. The results of multilevel mediation models showed that higher daily stress was related to within-day change in calmness from morning to evening, resulting in less calmness in the evening within persons. Less calmness in the evening, in turn, was related to poorer nightly sleep quality within persons. As expected, higher NED predicted a less negative within-person link between daily stress and calmness in the evening, thereby attenuating the indirect effect of daily stress on nightly sleep quality through calmness. This effect held when we controlled for mean negative emotions and depression. The results provide support for a diathesis-stress model of NED, and hence, for NED as a protective factor that helps to explain why some individuals remain more resilient during times of stress than others.
Network Reconstruction in Terms of the Priori Structure Information

In this paper, we investigate the reconstruction of networks based on priori structure information by the Element Elimination Method (EEM). We firstly generate four types of synthetic networks as small-world networks, random networks, regular networks and Apollonian networks. Then, we randomly delete a fraction of links in the original networks. Finally, we employ EEM, the resource allocation (RA) and the structural perturbation method (SPM) to reconstruct four types of synthetic networks with 90% priori structure information. The experimental results show that, comparing with RA and SPM, EEM has higher indices of reconstruction accuracy on four types of synthetic networks. We also compare the reconstruction performance of EEM with RA and SPM on four empirical networks. Higher reconstruction accuracy, measured by local indices of success rates, could be achieved by EEM, which are improved by 64.11 and 47.81%, respectively.
Neuroscience Concepts Changed Teachers’ Views of Pedagogy and Students

Advances in neuroscience reveal how individual brains change as learning occurs. Translating this neuroscience into practice has largely been unidirectional, from researchers to teachers. However, how teachers view and incorporate neuroscience ideas in their classroom practices remains relatively unexplored. Previously fourteen non-science teachers participated in a 3-week three credit graduate course focusing on foundational ideas in neuroscience. The current work was undertaken to gain insight into if and how individual teachers choose to later apply the proposed set of educational neuroscience concepts (ENCs) in their classrooms. This qualitative follow-up study examined commonalities in how teachers of diverse ages and subjects utilized their new neuroscience understandings. To this end, a year after the course, all participants assessed their perceived usefulness of the ENCs in a survey. Six of those teachers permitted classroom observations and participated in interviews that focused on how the ENCs may have influenced their lesson planning and teaching. The survey revealed that irrespective of subject areas or grade levels taught, teachers found the ENCs useful as organizing principles for their pedagogy now and in the future. Overall teachers estimated that the ENCs’ influence on lesson design had increased from 51% prior to the course to an estimated 90% for future lessons. A cross-case analysis of classroom observations and interviews revealed how teachers used ENCs to inform their pedagogical decisions, organize actions in their classroom, influence their understanding of students, and respond to individual contexts. Teachers recognized the importance of student agency for engaging them in the learning process. The ENCs also offered teachers explanations that affirmed known practices or helped justify exploring untried techniques. The foundational neuroscience concepts offered a small group of teachers a lens to reconsider, re-envision and re-design their lessons. Some teachers applied these ideas more broadly or frequently than others. This case study provided insights into how teachers can directly apply neuroscience knowledge to their practice and views of students.
Time Spent on School-Related Activities at Home During the Pandemic: A Longitudinal Analysis of Social Group Inequality Among Secondary School Students

Substantial educational inequalities have been documented in Germany for decades. In this article, we examine whether educational inequalities among children have increased or remained the same since the school closures of spring 2020 due to the COVID-19 pandemic. Our perspective is longitudinal: We compare the amount of time children in secondary schools spent on school-related activities at home before the pandemic, during school closures, and immediately after returning to in-person learning. We operationalize family socio-economic status using the highest parental educational attainment. Based on the theoretical assumption that the pandemic affected everyone equally, we formulate a hypothesis of equalization during the first period of school closures. For the period thereafter, however, we assume that parents with a low level of education had more difficulties bearing the additional burden of supervising and supporting their children’s learning activities. Thus, for that period, we postulate an increase in educational inequality. To study our hypotheses, we use data from the 2019 wave of the SOEP and the SOEP-CoV study, both of which are probability samples. The SOEP-CoV study provides a unique database, as it was conducted during the lockdown of spring 2020 and in the following month. For statistical analysis, we use probit regressions at three measurement points (in 2019, in 2020 during the school closures, and in the month after closures). The comparison of these three time points makes our analysis and findings unique in the research on education during the COVID-19 pandemic, in particular with regard to Germany-wide comparisons. Our results confirm the hypothesis of equalization during the first school closures and the hypothesis of an increase in educational in the subsequent period. Our findings have direct policy implications regarding the need to further expand support systems for children.
Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data

Bananas (Musa spp.) are some of the most important fruit crops in the world, contributing up to US$10 billion in export values annually. In this study, we use high-throughput sequencing to obtain genomic resources of high-copy DNA molecules in bananas. We sampled 13 wild species and eight cultivars that represent the three genera (Ensete, Musa, and Musella) of the banana family (Musaceae). Their plastomic, 45S rDNA, and mitochondrial scaffolds were recovered from genome skimming data. Two major clades (Clades I & II) within Musa are strongly supported by the three genomic compartment data. We document, for the first time, that the plastomes of Musaceae have expanded inverted repeats (IR) after they diverged from their two close relatives, Heliconiaceae (the lobster-claws) and Strelitziaceae (the traveler's bananas). The presence/absence of rps19 within IR regions reinforces the two intra-generic clades within Musa. Our comparisons of the bananas' plastomic and mitochondrial DNA sequence trees aid in identifying hybrid bananas' parentage. As the mitochondrial genes of Musa have elevated substitution rates, paternal inheritance likely plays an influential role on the Musa mitogenome evolution. We propose genome skimming as a useful method for reliable genealogy tracing and phylogenetics in bananas.
Fuzhenghefuzhiyang Formula (FZHFZY) Improves Epidermal Differentiation via Suppression of the Akt/mTORC1/S6K1 Signalling Pathway in Psoriatic Models

Psoriasis is a chronic proliferative skin disorder characterised by abnormal epidermal differentiation. The Fuzhenghefuzhiyang (FZHFZY) formula created by Chuanjian Lu, a master of Chinese medicine in dermatology, has been external used in the Guangdong Provincial Hospital of Chinese Medicine for the treatment of psoriasis, but its mechanisms of action against psoriasis remain poorly understood. This study involved an exploration of the effects of FZHFZY on epidermal differentiation and its underlying mechanisms in interleukin (IL)-17A/IL-22/interferon (IFN)-γ/tumour necrosis factor (TNF)-α–stimulated HaCaT cells and in a mouse model of imiquimod (IMQ)-induced psoriasis. Cell viability was assessed by MTT assay. Epidermal differentiation was detected by reverse-transcription polymerase chain reaction and western blotting. Histological evaluation of the skin tissue was performed via haematoxylin and eosin staining, and the Akt/mTORC1/S6K1 pathway was analysed by western blotting. FZHFZY inhibited proliferation and improved epidermal differentiation in IL-17A/IL-22/IFN-γ/TNF-α–induced HaCaT cells. FZHFZY ameliorated symptoms of psoriasis, regulated epidermal differentiation and inhibited phosphorylation of the Akt/mTORC1/S6K1 pathway in the skin of mice with imiquimod-induced psoriasis. Our results suggest that FZHFZY may exhibit therapeutic action against psoriasis by regulating epidermal differentiation via inhibition of the Akt/mTORC1/S6K1 pathway.
Identifying New Factors Associated With Cognitive Decline and Delirium After Transcatheter Aortic Valve Implantation: A Study Protocol

Background: Transcatheter aortic valve implantation (TAVI) has become the standard-of-care for treatment of severe symptomatic aortic stenosis and is also being increasingly recommended for low-risk patients. While TAVI boasts positive post-procedural outcomes, it is also associated with cognitive complications, namely delirium and cognitive decline. There is a pressing need for accurate risk tools which can identify TAVI patients at risk of delirium and cognitive decline, as risk scores designed for general cardiovascular surgery fall short. The present effect-finding exploratory study will assess the utility of various measures in the context of aging and frailty in predicting who will and who will not develop delirium or cognitive impairment following TAVI. The measures we propose include gait, visual symptoms, voice, swallowing, mood and sleep. Methods: This is an observational prospective cohort study focused on identifying pre-procedural risk factors for the development of delirium and cognitive decline following TAVI. Potential risk factors will be measured prior to TAVI. Primary outcomes will be post-procedure cognitive decline and delirium. Secondary outcomes include activities of daily living, quality of life, and mortality. Delirium presence will be measured on each of the first 2 days following TAVI. All other outcomes will be assessed at 3-, 6-, and 12-months post-operatively. A series of logistic regressions will be run to investigate the relationship between potential predictors and outcomes (presence vs. absence of either delirium or cognitive decline). Discussion: This study will assess the strengths of associations between a range of measures drawn from frailty and aging literature in terms of association with cognitive decline and delirium following TAVI. Identified measures can be used in future development of TAVI risk prediction models, which are essential for the accurate identification of cognitive at-risk patients and successful application of pre-procedural interventions. Clinical Trial Registration: This trial is registered with the Australian New Zealand Clinical Trials Registry. [https://bit.ly/2PAotP5], [ACTRN12618001114235].
Changes in Wnt and TGF-β Signaling Mediate the Development of Regorafenib Resistance in Hepatocellular Carcinoma Cell Line HuH7

Hepatocellular carcinoma (HCC) is an aggressive, chemo resistant neoplasm with poor prognosis and limited treatment options. Exploring activated pathways upon drug treatment can be used to discover more effective anticancer agents to overcome therapy resistance and enhance therapeutic outcomes for patients with advanced HCC. Human tumor-derived cell lines recapitulate HCC diversity and are widely used for studying mechanisms that drive drug resistance in HCC. In this study, we show that regorafenib treatment activates Wnt/β-catenin signaling only in hepatoblast-like HCC cell lines and induces enrichment of markers associated with hepatic stem/progenitor cells. Moreover, activation of Wnt/β-catenin signaling via Wnt3a/R-Spo1 treatment protects these cells from regorafenib induced apoptosis. On the other hand, regorafenib resistant cells established by long-term regorafenib treatment demonstrate diminished Wnt/β-catenin signaling activity while TGF-β signaling activity of these cells is significantly enhanced. Regorafenib resistant cells (RRCs) also show increased expression of several mesenchymal genes along with an induction of CD24 and CD133 cancer stem cell markers. Moreover, regorafenib resistant cells also exhibit significantly augmented in vitro and in vivo migration capacity which could be reversed by TGF-β type 1 receptor (TGFb -R1) inhibition. When combined with regorafenib treatment, TGFβ-R1 inhibition also significantly decreased colony formation ability and augmented cell death in resistant spheroids. Importantly, when we knocked down TGFβ-R1 using a lentiviral plasmid, regorafenib resistant cells entered senescence indicating that this pathway is important for their survival. Treatment of RRCs with TGFβ-R1 inhibitor and regorafenib significantly abolished pSTAT3, pSMAD2 and pERK (44/42) expression suggesting the involvement of both canonical and non-canonical pathways. In conclusion, our data suggest that HCC tumors with aberrant activation in the Wnt/β-catenin pathway, might have higher intrinsic regorafenib resistance and the inhibition of this pathway along with regorafenib administration might increase regorafenib-induced cell death in combinational therapies. However, to resolve acquired regorafenib resistance developed in HCC patients, the combined use of TGF-β pathway inhibitors and Regorafenib constitute a promising approach that can increase regorafenib sensitization and prevent tumor recurrence. Graphical Abstract Wnt and TGF-β pathways mediate the regorafenib resistance.
Toward More Robust Hand Gesture Recognition on EIT Data

Striving for more robust and natural control of multi-fingered hand prostheses, we are studying electrical impedance tomography (EIT) as a method to monitor residual muscle activations. Previous work has shown promising results for hand gesture recognition, but also lacks generalization across multiple sessions and users. Thus, the present paper aims for a detailed analysis of an existing EIT dataset acquired with a 16-electrode wrist band as a prerequisite for further improvements of machine learning results on this type of signal. The performed t-SNE analysis confirms a much stronger inter-session and inter-user variance compared to the expected in-class variance. Additionally, we observe a strong drift of signals within a session. To handle these challenging problems, we propose new machine learning architectures based on deep learning, which allow to separate undesired from desired variation and thus significantly improve the classification accuracy. With these new architectures we increased cross-session classification accuracy on 12 gestures from 19.55 to 30.45%. Based on a fundamental data analysis we developed three calibration methods and thus were able to further increase cross-session classification accuracy to 39.01, 55.37, and 56.34%, respectively.
Interactive Urban Play to Encourage Active Mobility: Usability Study of a Web-Based Augmented Reality Application

Owing to increasing cases of sedentary lifestyles and their negative impact on health, practical solutions are needed to address the physical and mental wellbeing of citizens and to enhance their standard of living. Among the problems are premature mortality rates caused by physical inactivity, which leads to chronic diseases. Innovative solutions are needed to address many of the problems that we face as a society. Location-based games have been identified as effective solutions for increasing physical activity, enhancing social interaction, and exploration in urban environments. In this pilot study, we explore how to encourage active mobility (walking and cycling) through urban play by integrating technology into the built environment. We examined the usability of a web-based augmented reality application in providing interactive experience to users as they explored the urban environment looking for tasks. Overall, participants’ perceptions of the usability of the application were positive; they enjoyed how the application revealed the tasks at each location and all the checkpoints at the different locations had at least a couple of visitors. We present limitations and future research directions.
The Phage T4 Antiholin RI Has a Cleavable Signal Peptide, Not a SAR Domain

Holin/endolysin-mediated lysis of phage T4 of Escherichia coli is tightly regulated by the antiholins RI and RIII. While regulation by the cytoplasmic RIII plays a minor role, the periplasmic antiholin RI binds tightly to the holin T and is believed to directly sense periplasmic phage DNA from superinfections as a trigger for the inhibition of lysis. RI has been reported to contain a non-cleavable signal peptide that anchors the protein to the membrane. Lysis is believed to be induced at some stage by a membrane depolarization that causes a release of RI into the periplasm without cleavage of the signal anchor. For the current model of phage lysis induction, it is thus a fundamental assumption that the N-terminal trans-membrane domain (TMD) of RI is such a signal anchor release (SAR) domain. Here we show that, in contrast to previous reports, this domain of RI is a cleavable signal peptide. RI is processed and released into the periplasm as a mature protein, and inactivation of its signal peptidase cleavage site blocks processing and membrane release. The signal peptide of RI can also mediate the normal translocation of a well-characterized Sec substrate, PhoA, into the periplasm. This simplifies the current view of phage lysis regulation and suggests a fundamentally different interpretation of the recently published structure of the soluble domains of the RI–T complex.