Miracle-dz/UniFAR-FTUs huggingface dataset:
New spectral indicator Potato Productivity Index based on Sentinel-2 data to improve potato yield prediction: a machine learning approach

ABSTRACT The potato (Solanum tuberosum L.) is one of the most important food crops and is consumed by more than a billion people worldwide. Despite the fact that crop growth models are widely used to optimize crop management and agricultural decision-making, they fail to provide spatial information, whereas satellite-based methods do, and in a cost-effective manner. In order to improve satellite-based crop yield prediction models, we developed a methodology based on Sentinel-2 (S2) data using Machine Learning (ML) techniques. In addition, we included and compared the commonly used Normalized Difference Vegetation Index (NDVI) to a newly developed spectral indicator, the Potato Productivity Index (PPI). Our results showed the capacity of our ML models to predict potato yield with great accuracy (coefficient of determination (R2) = 0.77 and Root Mean Square Error (RMSE) = 15.42%), using S2 bands 2, 3, 4, 5, 8A, and 9, as well as the PPI index. This index aims to provide information concerning plant photosynthetic activity as well as its water stress. The Random Forest (RF) model using the S2 bands and the PPI index as predictors obtained better predictive results (R2 = 0.77, RMSE = 15.42%) for potato crops than using S2 bands and NDVI (R2 = 0.66, RMSE = 16.88%). This study demonstrates the suitability of our models to predict potato yields in the region studied and improves on a previous approach presented by the same authors in terms of model interpretability and inter-annual variability.
L2-norm prototypical networks for tackling the data shift problem in scene classification

ABSTRACT Currently, most scene classification algorithms are trained and evaluated based on a single dataset. However, practical applications are not usually restricted to specific satellite platforms or datasets. Researchers generally train a model on one dataset and require the model to perform tasks with another dataset, leading to a data shift problem and performance decrease in practical applications. To address this problem, this study presents a metric-based few-shot classification method with -norm prototypical networks. Specifically, a carefully designed -norm layer was introduced into prototypical networks. The proposed -norm layer applies -norm operations to prototypes and query features to mitigate the length fluctuations caused by the data shift problem. With this layer, the -norm prototypical networks maintain the ability to identify novel classes and limit the effects of data discrepancies. The proposed -norm layer improves the classification accuracy by 0.42% to 2.41% on various public datasets. Moreover, -norm prototypical networks outperform other methods by 0.02% to 34.38%. Comprehensive experiments consistently demonstrate the advantages of the proposed method in tackling the data shift problem.
Handbook of Environmental and Ecological Statistics.

models using MCMC the book turns to WinBUGS, a wellestablished piece of software, for the integrated nested Laplace approximation (INLA) uses R-INLA. In the years since the book’s publication, the computational toolbox has continued to expand. The sp package has been augmented with the sf package, which provides a simple and flexible interface that will be familiar to users of the tidyverse. Mapping in R has continued to improve through the development of tmap and leaflet. The probabilistic programming language Stan and the associated R package rstan allows more efficient Bayesian inferences using Hamiltonian Monte Carlo. These packages would be a welcome addition to a second edition of this book. Although the methodology presented in the book is well explained, the code to reproduce most of the approaches is not provided. This is an unfortunate omission, as it would have provided means for researchers and practitioners to apply the methods presented to their own investigations easily and unambiguously. It also would have aided instructors who wish to pull chapters from this book for use in an applied course. Overall, this book provides an overview of the rich variety of spatial epidemiology methods and their application. For readers coming from general statistics, the attention paid to issues such as misalignment, ecological bias, and the interpretation of results will be particularly useful. In the years since the publication of this handbook, the field has continued to evolve. A present survey of the discipline would include a discussion of new data sources, machine learning approaches, and modern software packages for spatial analysis, as well as a supplement containing the code necessary to apply the methods presented. With these additions, this handbook stands as a valuable resource for researchers and professionals interested in solving new challenges in spatial epidemiology and public health surveillance.
Young children’s conceptions of morality in a South African context

The aim of the study was to explore children’s conceptions of morality, specifically the meanings children assigned to situations of morality. The participants were eight to eleven-year-old children (n = 8; female = 5, male = 3) who attended a primary school in KwaZulu-Natal. The children completed vignettes depicting moral dilemmas involving the following hypothetical scenarios: scenario 1 = seeking revenge; scenario 2 = breach of a contract. Thematic analysis of the data uncovered three themes: (i) sense of right or wrong; (ii) ethics of care; and (iii) ideas about fairness. Findings reveal that the young children had advanced conceptions of morality and understandings of justice, ethics of care, and notions of fairness. It emerged that their moral reasoning, moral judgements, moral attributions, and moral emotions are intersecting in nature and are underpinned by the African values of Ubuntu.
Field calibration using the energy distribution of a free‐space field ionization

Utilizing free‐space field ionization, a new method of field calibration for field ion emitters has been developed. Plotting the differences of relative energy deficits of free‐space ionized H2, D2, or Kr for sets of various applied voltages V against the logarithm of the voltage ratios yields a field factor k from which the surface field F0=V/krtip is obtained with 3% accuracy. Refinement of this method also enabled us to determine the local radii of the specimen tip. In addition to new and more reliable data of evaporation fields of various materials, such as W, Mo, Rh, Ir, Pt, and Ni, it has revealed several significant facts on the geometrical shape of the emitter.
Role of Lipids in Morphogenesis of T-Cell Microvilli

T cells communicate with the environment via surface receptors. Cooperation of surface receptors regulates T-cell responses to diverse stimuli. Recently, finger-like membrane protrusions, microvilli, have been demonstrated to play a role in the organization of receptors and, hence, T-cell activation. However, little is known about the morphogenesis of dynamic microvilli, especially in the cells of immune system. In this review, I focus on the potential role of lipids and lipid domains in morphogenesis of microvilli. Discussed is the option that clustering of sphingolipids with phosphoinositides at the plasma membrane results in dimpling (curved) domains. Such domains can attract phosphoinositide-binding proteins and stimulate actin cytoskeleton reorganization. This process triggers cortical actin opening and bundling of actin fibres to support the growing of microvilli. Critical regulators of microvilli morphogenesis in T cells are unknown. At the end, I suggest several candidates with a potential to organize proteins and lipids in these structures.
Psychological Outcomes in Children and Early Adolescents With Type 1 Diabetes Following Pediatric Diabetes Summer Camp: A 3-Month Follow-Up Study

Objective: The aim of this study was to assess general psychosocial adjustment to diabetes and perceived disease management among patients with type 1 diabetes (T1D) and their parents before and after patients' participation in a diabetes summer camp. Methods: In this follow-up study, 20 children and adolescents with T1D (eight boys; mean age = 11.01 ± 0.94 years; mean diabetes duration = 3.02 ± 2.27) attending a southern Italian diabetic center, along with their parents, were assessed prior to and 3 months after the youths participated in a 1 week camp-based intervention involving didactic and interactive child-centered education and recreational activities. Patients and their parents completed measures assessing patients' quality of life and strategies employed by patients to cope with pain. Patients also completed measures evaluating their diabetes psychosocial adjustment, diabetes self-efficacy management, and illness perception; also, their parents completed measures of caregivers' perceived diabetes burden and treatment satisfaction. Youths' glycated hemoglobin (HbA1c) and standardized body mass index (z-BMI) values were also assessed. Within-subjects repeated-measures analyses of variance evaluated pre- and post-camp changes. Results: Camp attendance showed no beneficial effects on glycemic control, as indicated by HbA1c values both before (7.02%) and after (7.28%) camp being lower than 7.5%. HbA1c values were found to have increased after camp (pre-camp = 7.02%, post-camp = 7.28%; p = 0.010), but since they still fell within an acceptable range, they did not reveal clinically relevant changes in glycemic control. No substantial significant improvement in psychosocial measures was observed in children or parents (all p > 0.05). According to the parents' evaluation, social support-seeking as a patient pain-coping strategy was slightly increased (p = 0.044) after attending the camp. Conclusions: This study does not provide empirical evidence of benefits of participating in a diabetes camp for either patients or their parents. These findings suggest that healthcare providers rethink such camps as an experience for youths with T1D that actively involves parents and that includes both youth- and parent-focused psychological interventions.
Development of a Health Information Technology Tool for Behavior Change to Address Obesity and Prevent Chronic Disease Among Adolescents: Designing for Dissemination and Sustainment Using the ORBIT Model

Health information technology (HIT) has not been broadly adopted for use in outpatient healthcare settings to effectively address obesity in youth, especially among disadvantaged populations that face greater barriers to good health. A well-designed HIT tool can deliver behavior change recommendations and provide community resources to address this gap, and the Obesity-Related Behavioral Intervention Trials (ORBIT) model can guide its development and refinement. This article reports the application of the ORBIT model to (1) describe the characteristics and design of a novel HIT tool (the PREVENT tool) using behavioral theory, (2) illustrate the use of stakeholder-centered “designing for dissemination and sustainability” principles, and (3) discuss the practical implications and directions for future research. Two types of stakeholder engagement (customer discovery and user testing) were conducted with end users (outpatient healthcare teams). Customer discovery interviews (n = 20) informed PREVENT tool components and intervention targets by identifying (1) what healthcare teams (e.g., physicians, dietitians) identified as their most important “jobs to be done” in helping adolescents who are overweight/obese adopt healthy behaviors, (2) their most critical “pains” and “gains” related to overweight/obesity treatment, and (3) how they define success compared to competing alternatives. Interviews revealed the need for a tool to help healthcare teams efficiently deliver tailored, evidence-based behavior change recommendations, motivate patients, and follow-up with patients within the constraints of clinic schedules and workflows. The PREVENT tool was developed to meet these needs. It facilitates prevention discussions, delivers tailored, evidence-based recommendations for physical activity and food intake, includes an interactive map of community resources to support behavior change, and automates patient follow-up. Based on Self-Determination Theory, the PREVENT tool engages the patient to encourage competence and autonomy to motivate behavior change. The use of this intentional, user-centered design process should increase the likelihood of the intended outcomes (e.g., behavior change, weight stabilization/loss) and ultimately increase uptake, implementation success, and long-term results. After initial tool development, user-testing interviews (n = 13) were conducted using a think-aloud protocol that provided insight into users' (i.e., healthcare teams) cognitive processes, attitudes, and challenges when using the tool. Overall, the PREVENT tool was perceived to be useful, well-organized, and visually appealing.
A Dual Systems Genetics Approach Identifies Common Genes, Networks, and Pathways for Type 1 and 2 Diabetes in Human Islets

Type 1 and 2 diabetes (T1/2D) are complex metabolic diseases caused by absolute or relative loss of functional β-cell mass, respectively. Both diseases are influenced by multiple genetic loci that alter disease risk. For many of the disease-associated loci, the causal candidate genes remain to be identified. Remarkably, despite the partially shared phenotype of the two diabetes forms, the associated loci for T1D and T2D are almost completely separated. We hypothesized that some of the genes located in risk loci for T1D and T2D interact in common pancreatic islet networks to mutually regulate important islet functions which are disturbed by disease-associated variants leading to β-cell dysfunction. To address this, we took a dual systems genetics approach. All genes located in 57 T1D and 243 T2D established genome-wide association studies (GWAS) loci were extracted and filtered for genes expressed in human islets using RNA sequencing data, and then integrated with; (1) human islet expression quantitative trait locus (eQTL) signals in linkage disequilibrium (LD) with T1D- and T2D-associated variants; or (2) with genes transcriptionally regulated in human islets by pro-inflammatory cytokines or palmitate as in vitro models of T1D and T2D, respectively. Our in silico systems genetics approaches created two interaction networks consisting of densely-connected T1D and T2D loci genes. The “T1D-T2D islet eQTL interaction network” identified 9 genes (GSDMB, CARD9, DNLZ, ERAP1, PPIP5K2, TMEM69, SDCCAG3, PLEKHA1, and HEMK1) in common T1D and T2D loci that harbor islet eQTLs in LD with disease-associated variants. The “cytokine and palmitate islet interaction network” identified 4 genes (ASCC2, HIBADH, RASGRP1, and SRGAP2) in common T1D and T2D loci whose expression is mutually regulated by cytokines and palmitate. Functional annotation analyses of the islet networks revealed a number of significantly enriched pathways and molecular functions including cell cycle regulation, inositol phosphate metabolism, lipid metabolism, and cell death and survival. In summary, our study has identified a number of new plausible common candidate genes and pathways for T1D and T2D.
Increasing Embryonic Morphogen Nodal Expression Suggests Malignant Transformation in Colorectal Lesions and as a Potential Marker for CMS4 Subtype of Colorectal Cancer

Nodal, an embryonic morphogen in TGF-β family, is related with tumorigenicity and progression in various tumors including colorectal cancer (CRC). However, the difference of Nodal expression between CRC and colorectal polyps has not yet been investigated. Besides, whether Nodal can be used as a marker for consensus molecular subtype classification-4 (CMS4) of CRC is also worth studying. We analyzed Nodal expression in patients of CRC (161), high-grade intraepithelial neoplasia (HGIN, 28) and five types of colorectal polyps (116). The Nodal expression difference among groups and the association between Nodal expression and clinicopathological features were analyzed. Two categories logistic regression model was used to predict the odds ratio (OR) of risk factors for high tumor-stroma percentage (TSP), and ROC curve was used to assess the diagnostic value of Nodal in predicting high TSP in CRC. We found that Nodal expression was significantly elevated in CRC and HGIN (p < 0.0001). The increased expression of Nodal was related with high TSP, mismatch repair-proficient (pMMR) status, lymph node metastasis and advanced AJCC stage (p < 0.05). Besides, Nodal expression was the only risk factor for high TSP (OR = 6.94; p < 0.001), and ROC curve demonstrated that Nodal expression was able to efficiently distinguish high and low TSP. In conclusion, different expression of Nodal between CRC/HGIN and benign lesions is suggestive of a promoting role for Nodal in colorectal tumor progression. Besides, Nodal might also be used as a potential marker for CMS4 subtype of CRC.
Severe Vitamin D Deficiency Is Associated With Increased Expression of Inflammatory Cytokines in Painful Diabetic Peripheral Neuropathy

Background: The exact pathogenic mechanism of the painful diabetic peripheral neuropathy (DPN) is poorly understood. Our study aimed to evaluate the association amongst vitamin D status, inflammatory cytokines, and painful DPN. Methods: A total of 483 patients were divided into three groups, i.e., diabetes without DPN (no-DPN, n = 86), diabetes with painless DPN (painless DPN, n = 176) and diabetes with painful DPN (painful DPN, n = 221) groups. Basic information and laboratory results were collected. The concentrations of vitamin D (25-hydroxyvitamin D), high-sensitivity C-reactive protein, interleukin (IL)-2, IL-4, IL-6, IL-10, tumor necrosis factor-α (TNF-α), and interferon-γ (IFN-γ) were also measured. Results: The prevalence of severe vitamin D deficiency (<10 ng/mL) was more common in the painful DPN group than in the painless DPN and no-DPN groups (25.8,12.5, and 8.1%, respectively, P < 0.01). Cases in the painful DPN group had significantly higher concentrations of IL-6 (P < 0.01) and TNF-α (P < 0.01) than those in the two other groups. The multivariate logistic analysis showed that severe vitamin D deficiency, IL-6, and TNF-α were independent risks for painful DPN after adjusting for confounding factors. Furthermore, the vitamin D status had significantly negative correlations with IL-6 (r = −0.56, P < 0.01) and TNF-α (r = −0.47, P < 0.01) levels. Conclusion: Severe vitamin D deficiency was an independent risk factor for the painful DPN. Severe vitamin D deficiency status may play a role in the painful DPN pathogenesis through elevated IL-6 and TNF-α levels.
Satellite Glial Cells in Pain Research: A Targeted Viewpoint of Potential and Future Directions

Chronic pain is known to be caused by sensitization within the pain circuits. An imbalance occurs between excitatory and inhibitory transmission that enables this sensitization to form. In addition to neurons, the contribution of central glia, especially astrocytes and microglia, to the pathogenesis of pain induction and maintenance has been identified. This has led to the targeting of astrogliosis and microgliosis to restore the normal functions of astrocytes and microglia to help reverse chronic pain. Gliosis is broadly defined as a reactive response of glial cells in response to insults to the central nervous system (CNS). The role of glia in the peripheral nervous system (PNS) has been less investigated. Accumulating evidence, however, points to the contribution of satellite glial cells (SGCs) to chronic pain. Hence, understanding the potential role of these cells and their interaction with sensory neurons has become important for identifying the mechanisms underlying pain signaling. This would, in turn, provide future therapeutic options to target pain. Here, a viewpoint will be presented regarding potential future directions in pain research, with a focus on SGCs to trigger further research. Promising avenues and new directions include the potential use of cell lines, cell live imaging, computational analysis, 3D tissue prints and new markers, investigation of glia–glia and macrophage–glia interactions, the time course of glial activation under acute and chronic pathological pain compared with spontaneous pain, pharmacological and non-pharmacological responses of glia, and potential restoration of normal function of glia considering sex-related differences.
The Integration Preference of Sleeping Beauty at Non-TA Site Is Related to the Transposon End Sequences

Recently, we proved that Sleeping Beauty (SB) transposon integrates into non-TA sites at a lower frequency. Here, we performed a further study on the non-TA integration of SB and showed that (1) SB can integrate into non-TA sites in HEK293T cells as well as in mouse cell lines; (2) Both the hyperactive transposase SB100X and the traditional SB11 catalyze integrations at non-TA sites; (3) The consensus sequence of the non-TA target sites only occurs at the opposite side of the sequenced junction between the transposon end and the genomic sequences, indicating that the integrations at non-TA sites are mainly aberrant integrations; and (4) The consensus sequence of the non-TA target sites is corresponding to the transposon end sequence. The consensus sequences changed following the changes of the transposon ends. This result indicated that the interaction between the SB transposon end and genomic DNA (gDNA) may be involved in the target site selection of the SB integrations at non-TA sites.
Changes in Resting-State Functional Connectivity of Cerebellum in Amnestic Mild Cognitive Impairment and Alzheimer’s Disease: A Case-Control Study

This case-control study is aimed to investigate the correlation of altered functional connectivity (FC) in cerebellum with cognitive impairment in amnestic mild cognitive impairment (aMCI) and Alzheimer’s disease (AD). The morphometric and resting-state FC MRI analysis including 46 participants with AD, 32 with aMCI and 42 age-matched normal controls (NCs) were conducted. We compared the cerebellar gray matter volume and cerebellar FC with cerebral cortical regions among three groups. To investigate the relationship of cerebellar FC with cognition, we measure the correlation of significant altered FC and individual cognitive domain. No significant morphometric differences of cerebellum was observed across three groups. The patients with AD had weaker cerebral cortical FCs in bilateral Crus I and left VIIb compared to NCs, and in bilateral Crus I compared to patients with aMCI. For patients with aMCI, the weaker FC were found between right Crus I, left VIIb and cerebral cortical regions compared to NCs. The strength of left cerebellar FC positively correlated with specific cognitive subdomains, including memory, executive function, visuospatial function, and global cognition in AD and aMCI. These findings demonstrated the alteration of cerebellar FC with cerebral cortical regions, and the correlation of cerebellar FC and cognitive impairment in AD and aMCI.