Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs (mRNAs) for cleavage or repressing translation of specific mRNAs. The first miRNA identified in plants, miRNA156 (miR156), targets the SQUAMOSA promoter-binding protein-like (SPL) transcription factors, which play critical roles in plant phase transition, flower and plant architecture, and fruit development. We identified multiple copies of MIR156 and SPL in the rice, Brachypodium, sorghum, maize, and foxtail millet genomes. Sequence and chromosomal synteny analysis showed that both MIR156s and SPLs are conserved across species in the grass family. Analysis of expression data of the SPLs in eleven juvenile and adult rice tissues revealed that four non-miR156-targeted genes were highly expressed and three miR156-targeted genes were only slightly expressed in all tissues/developmental stages. The remaining SPLs were highly expressed in the juvenile stage, but their expression was lower in the adult stage. It has been proposed that under strong selective pressure, non-miR156-targeted mRNA may be able to re-structure to form a miRNA-responsive element. In our analysis, some non-miR156-targeted SPLs (SPL5/8/10) had gene structure and gene expression patterns similar to those of miR156-targeted genes, suggesting that they could diversify into miR156-targeted genes. DNA methylation profiles of SPLs and MIR156s in different rice tissues showed diverse methylation patterns, and hypomethylation of non-CG sites was observed in rice endosperm. Our findings suggested that MIR156s and SPLs had different origination and evolutionary mechanisms: the SPLs appear to have resulted from vertical evolution, whereas MIR156s appear to have resulted from strong evolutionary selection on mature sequences.
Therapy Dose Mediates the Relationship Between Buprenorphine/Naloxone and Opioid Treatment Outcomes in Youth Receiving Medication for Opioid Use Disorder Treatment

Background: Evidence-based interventions for treating opioid use disorder (OUD) in youth are limited and little is known about specific and general mechanisms of OUD treatments and how they promote abstinence. Methods: The present study used data from the NIDA-CTN-0010 trial to evaluate the mediating effects of psychosocial treatment-related variables (therapy dose and therapeutic alliance) on end-of-treatment opioid abstinence in a sample of youth with OUD (n = 152, 40% female, mean age = 19.7 years) randomized to receive either 12-weeks of treatment with Bup/Nal (“Bup-Nal”) or up to 2 weeks of Bup/Nal detoxification (“Detox”) with both treatment arms receiving weekly individual and group drug counseling ± family therapy. Results: Participants in the Bup-Nal group attended more therapy sessions (16 vs 6 sessions), had increased therapeutic alliance at week-4, and had less opioid use by week-12 compared to those in the Detox group. In both treatment arms, youth who attended more therapy sessions were less likely to have a week-12 opioid positive urine. In a multiple mediator model, therapy dose mediated the association between treatment arm and opioid abstinence. Conclusions: These findings provide preliminary support for a “dose-response” effect of addiction-focused therapy on abstinence in youth OUD. Further, the results identified a mediating effect of therapy dose on the relationship between treatment assignment and opioid treatment outcomes, suggesting that extended Bup-Nal treatment may enhance abstinence, in part, through a mechanism of therapy facilitation, by increasing therapy dose during treatment.
Normative and Psychometric Characteristics of the Health and Behavior Inventory Among Children With Mild Orthopedic Injury Presenting to the Emergency Department: Implications for Assessing Postconcussive Symptoms Using the Child Sport Concussion Assessment Tool 5th Edition (Child SCAT5)

Objective: The study sought to present normative and psychometric data and reliable change formulas for the Health and Behavior Inventory (HBI), a postconcussive symptom rating scale embedded in the Child Sport Concussion Assessment Tool 5th edition (Child SCAT5). Design: Prospective cohort study with longitudinal follow-up. Setting: Pediatric emergency departments (EDs). Participants: As part of 3 studies conducted in the United States and Canada between 2001 and 2019, 450 children aged 8 to 16 years with mild orthopedic injuries were recruited during ED visits and assessed postacutely (M = 9.38 days, SD = 3.31) and 1 month and 3 months postinjury. Independent variables were rater (child vs parent), sex, and age at injury. Main Outcome Measure: HBI ratings. Methods: Children and parents rated children's symptoms at each time point; parents also rated children's preinjury symptoms retrospectively. Normative data (mean, SD, skewness, kurtosis, and percentiles) were computed for child and parent ratings. Internal consistency was assessed using Cronbach alpha (α), and test–retest reliability and interrater agreement were assessed with intraclass correlations (ICCs). Reliable change formulas were computed using linear regression and mixed models. Results: HBI ratings were positively skewed. Mean ratings and percentiles were stable over time. Child and parent ratings demonstrated good-to-excellent internal consistency (α 0.76-0.94) and moderate-to-good test–retest reliability (ICC 0.51-0.76 between adjacent assessments). However, parent–child agreement was poor to moderate (ICC 0.31-0.69). Conclusions: The HBI demonstrates acceptable normative and psychometric characteristics. Modest parent–child agreement highlights the importance of multiple informants when assessing postconcussive symptoms. The results will facilitate the use of the HBI in research and clinical practice.
A brief review on Ion Exchange Chromatography

Ion exchange chromatography is probably the most powerful and classic type of liquid chromatography. The popularity of ion exchange chromatography has been increased in recent years because this technique allows analysis of wide range of molecules in pharmaceutical, biotechnology, environmental, agricultural and other industries for water purification to separation of various antibiotics from fermentation broths which will enhance the yields and reduce the production time for industrial process. The main objective of this particular study is to develop some understanding for the process of ion exchange and helps to determine whether or not ion exchange will be useful for a particular application. This topic includes background, theory, instrumentation, application which covers both the production of the ion exchange substance, a resin and its operation depending on the condition of matrix during use.
DDX10 promotes human lung carcinoma proliferation by U3 small nucleolar ribonucleoprotein IMP4

Lung cancer is a common tumor and a leading cause of death worldwide. DEAD/H box RNA helicases (DDX) include several family members which regulate mRNA translation in cancer cells. In this study, we demonstrated that DEAD/H box RNA helicase 10 (DDX10) was significantly upregulated in lung cancer tissues compared with adjacent nontumor tissues.
Nonlinear Absorption and Fluorescence in ZnO and ZnO–Au Nanostructures

This paper investigates whether coupling gold nanoparticles to nanostructured zinc oxide enhances fluorescence emission, to produce efficient nanoscale UV emitters that radiate through nonlinear optical absorption processes. The z‐scan technique is used to measure nonlinear absorption simultaneously with measurements of nonlinear‐absorption‐induced fluorescence in zinc oxide nanostructures and hybrid zinc oxide–gold nanostructures. This allows for better determination of the nonlinear excitation and energy dissipation pathways. The measurements show that the nonlinear absorption of the hybrid structures is enhanced by up to two orders of magnitude compared to the pure zinc oxide nanostructures. However, it is found that the increase in nonlinear absorption does not correspond to an equivalent increase in fluorescence due to the competition between two‐photon absorption and excited state absorption.
The Lived Experience of Pain and Depression Symptoms during Pregnancy.

Background: Depressive symptoms and pain are prevalent during pregnancy. Untreated pain and depressive symptoms occurring together may have a negative effect on maternal and newborn outcomes, yet little is known about women’s experiences with pain and depressive symptoms during pregnancy. The purpose of this study is to describe the lived experience of depressive symptoms and pain occurring in women during the third trimester of pregnancy. Methods: A descriptive phenomenological study was conducted. Women during postpartum were recruited from a previous cross-sectional study of women in their third trimester which evaluated the relationship between pain, depression, and quality of life. Twenty-four women entered their responses into an online secure research website. These data were analyzed using Colaizzi’s method of descriptive phenomenological analysis. Results: Four themes emerged that described the essence of women’s experiences with both pain and depressive symptoms Pregnancy: Feeling Minimized, Unheard and Overwhelmed; Attempting or Trying but not Treated: Living with Pain and Pain Interference; Pain, Sleep Loss, and Suffering; and Pain and Depressive Symptoms: Helpless, Hopeless, and Suffering. Clinical Implications: If a woman presents with pain, additional nursing assessments of her sleep and emotional state may be needed. Likewise, a positive depression symptom screening suggests the need for a more in-depth exploration of pain, pain interference, poor sleep, and mental health symptoms. As these women perceive their pregnancy as minimized, nurses may Julie-vignato@uiowa.edu. HHS Public Access Author manuscript MCN Am J Matern Child Nurs. Author manuscript; available in PMC 2022 January 01. Published in final edited form as: MCN Am J Matern Child Nurs. 2021 ; 46(4): 198–204. doi:10.1097/NMC.0000000000000724. A uhor M anscript
The risk of tooth loss in patients with diabetes: A systematic review and meta‐analysis

Abstract Aim The aim of this systematic review was to comprehensively and critically summarize and synthesize the risk of losing teeth among with diabetes mellitus (DM) compared to those without DM, as established in observational studies. Materials and methods MEDLINE‐PubMed and Cochrane databases were searched through a period from their inception through October 2020 to identify eligible studies. Papers that primarily evaluate the number of teeth in DM patients compared to non‐DM individuals were included. A descriptive analysis of the selected studies was conducted, and when feasible, a meta‐analysis was performed. The quality of the studies was assessed. Results A total of 1087 references were generated, and screening of the papers resulted in 10 eligible publications. A descriptive analysis demonstrated that six of these studies indicate a significantly higher risk of tooth loss in DM patients. This was confirmed by the meta‐analysis risk ratio of 1.63 95% CI (1.33; 2.00, p < 0.00001). Subgroup analysis illustrates that this is irrespective of the risk‐of‐bias assessment. The higher risk of tooth loss in DM patients was also higher when only DM type II patients or studies with a cross‐sectional design were considered. Patients with a poor DM control status presented a significantly increased risk of tooth loss. When the data were separated by the world continent where the study was performed, Asia and South America had numerically higher risks and a 95% CI that did not overlap with Europe and North America. Conclusion There is moderate certainty for a small but significantly higher risk of tooth loss in DM patients as compared to those without DM.
Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease

A large number of genetic variations have been identified to be associated with Alzheimer's disease (AD) and related quantitative traits. However, majority of existing studies focused on single types of omics data, lacking the power of generating a community including multi-omic markers and their functional connections. Because of this, the immense value of multi-omics data on AD has attracted much attention. Leveraging genomic, transcriptomic and proteomic data, and their backbone network through functional relations, we proposed a modularity-constrained logistic regression model to mine the association between disease status and a group of functionally connected multi-omic features, i.e. single-nucleotide polymorphisms (SNPs), genes and proteins. This new model was applied to the real data collected from the frontal cortex tissue in the Religious Orders Study and Memory and Aging Project cohort. Compared with other state-of-art methods, it provided overall the best prediction performance during cross-validation. This new method helped identify a group of densely connected SNPs, genes and proteins predictive of AD status. These SNPs are mostly expression quantitative trait loci in the frontal region. Brain-wide gene expression profile of these genes and proteins were highly correlated with the brain activation map of 'vision', a brain function partly controlled by frontal cortex. These genes and proteins were also found to be associated with the amyloid deposition, cortical volume and average thickness of frontal regions. Taken together, these results suggested a potential pathway underlying the development of AD from SNPs to gene expression, protein expression and ultimately brain functional and structural changes.
Making every contact count: recognising obesity in paediatric and young adult cardiology

Abstract Introduction: With increased survival, children with CHD are reaching adulthood, however, obesity amongst this cohort is an emerging problem. Making every contact count encourages clinicians to utilise contact to elicit behaviour change. The aim of this work was to identify whether the body habitus of children classified as obese was addressed during a clinical review. Methods: A retrospective observational cohort study was completed using a cardiology outpatient dataset from 2010 to 2019. Inclusion criteria are all children with a body mass index z score classified as obese (≥ 2 z scores). Individual electronic patient records were reviewed to identify long-term anthropometric measures including (i) recognition of body habitus, (ii) prescription of physical activity or dietary intervention, and (iii) referral to a weight management programme or dietitian. Results: From the cohort of 95 patients, 285 “obese clinical encounters” were identified, at the time of a cardiology clinic attendance. Of those, obesity was acknowledged in 25 clinic letters (8.65%), but only 8 used the correct terms “obese” or “obesity” (2.77%). Action to tackle obesity was recorded in 9.3% of cases with a direct referral to a dietitian being made on 3 occasions (1.04%). Conclusions: Body habitus is not being routinely addressed by cardiologists caring for paediatric and young adult cardiac patients. This study has recognised an alarmingly high incidence of missed opportunities to make every contact count, to manage those with obesity and associated risk factors.
Continuous learning of emergent behavior in robotic matter

Significance In the last century, robots have been revolutionizing our lives, augmenting human actions with greater precision and repeatability. Unfortunately, most robotic systems can only operate in controlled environments. While increasing the complexity of the centralized controller is an instinctive direction to enable robots that are capable of autonomously adapting to their environment, there are ample examples in nature where adaptivity emerges from simpler decentralized processes. Here we perform experiments and simulations on a modular and scalable robotic platform in which each unit is stochastically updating its own behavior to explore requirements needed for a decentralized learning strategy capable of achieving locomotion in a continuously changing environment or when undergoing damage. One of the main challenges in robotics is the development of systems that can adapt to their environment and achieve autonomous behavior. Current approaches typically aim to achieve this by increasing the complexity of the centralized controller by, e.g., direct modeling of their behavior, or implementing machine learning. In contrast, we simplify the controller using a decentralized and modular approach, with the aim of finding specific requirements needed for a robust and scalable learning strategy in robots. To achieve this, we conducted experiments and simulations on a specific robotic platform assembled from identical autonomous units that continuously sense their environment and react to it. By letting each unit adapt its behavior independently using a basic Monte Carlo scheme, the assembled system is able to learn and maintain optimal behavior in a dynamic environment as long as its memory is representative of the current environment, even when incurring damage. We show that the physical connection between the units is enough to achieve learning, and no additional communication or centralized information is required. As a result, such a distributed learning approach can be easily scaled to larger assemblies, blurring the boundaries between materials and robots, paving the way for a new class of modular “robotic matter” that can autonomously learn to thrive in dynamic or unfamiliar situations, for example, encountered by soft robots or self-assembled (micro)robots in various environments spanning from the medical realm to space explorations.
Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro

ABSTRACT Although promising for active immunization in cancer patients, dendritic cells (DCs) vaccines generated in vitro display high inter-individual variability in their immunogenicity, which mostly limits their therapeutic efficacy. Gut microbiota composition is a key emerging factor affecting individuals’ immune responses, but it is unknown how it affects the variability of donors’ precursor cells to differentiate into immunogenic DCs in vitro. By analyzing gut microbiota composition in 14 healthy donors, along with the phenotype and cytokines production by monocyte-derived DCs, we found significant correlations between immunogenic properties of DC and microbiota composition. Namely, donors who had higher α-diversity of gut microbiota and higher abundance of short-chain fatty acid (SCFAs) and SCFA-producing bacteria in feces, displayed lower expression of CD1a on immature (im)DC and higher expression of ILT-3, costimulatory molecules (CD86, CD40) proinflammatory cytokines (TNF-α, IL-6, IL-8) and IL-12p70/IL-10 ratio, all of which correlated with their lower maturation potential and immunogenicity upon stimulation with LPS/IFNγ, a well-known Th1 polarizing cocktail. In contrast, imDCs generated from donors with lower α-diversity and higher abundance of Bifidobacterium and Collinsella in feces displayed higher CD1a expression and higher potential to up-regulate CD86 and CD40, increase TNF-α, IL-6, IL-8 production, and IL-12p70/IL-10 ratio upon stimulation. These results emphasize the important role of gut microbiota on the capacity of donor precursor cells to differentiate into immunogenic DCs suitable for cancer therapy, which could be harnessed for improving the actual and future DC-based cancer therapies.
A highly conserved pocket on PP2A‐B56 is required for hSgo1 binding and cohesion protection during mitosis

The shugoshin proteins are universal protectors of centromeric cohesin during mitosis and meiosis. The binding of human hSgo1 to the PP2A‐B56 phosphatase through a coiled‐coil (CC) region mediates cohesion protection during mitosis. Here we undertook a structure function analysis of the PP2A‐B56‐hSgo1 complex, revealing unanticipated aspects of complex formation and function. We establish that a highly conserved pocket on the B56 regulatory subunit is required for hSgo1 binding and cohesion protection during mitosis in human somatic cells. Consistent with this, we show that hSgo1 blocks the binding of PP2A‐B56 substrates containing a canonical B56 binding motif. We find that PP2A‐B56 bound to hSgo1 dephosphorylates Cdk1 sites on hSgo1 itself to modulate cohesin interactions. Collectively our work provides important insight into cohesion protection during mitosis.
Opioid maintenance treatment in the Czech Republic, Norway and Denmark: a study protocol of a comparative registry linkage study

Introduction Opioid maintenance treatment (OMT) varies across settings and between countries. We plan to use data from several nationwide health and population registers to further improve the knowledge base established from earlier studies. Our aim is to study OMT adherence trajectories and to identify factors associated with improved outcomes for OMT patients across the Czech Republic, Norway and Denmark, in order to further improve OMT and our understanding of the key elements of treatment success. Methods and analysis The registry-based cohort approach across the three countries allows us to link data from a range of registers on the individual level, by using personal identifiers in nationwide cohorts of OMT and non-OMT patients and the general non-using populations. A total of ~21 500 OMT patients over the last two decades in all three countries will be included in the study. The following outcome variables (based on the International Classification of Diseases, 10th Revision codes) will be obtained from relevant registers: treatment adherence to OMT, comorbidity (somatic and mental health), and all-cause and cause-specific mortality. Outcomes of the country-specific analyses will be pooled. Ethics and dissemination The national OMT cohorts have been approved by the ethics committees in the respective countries. Data will be stored according to national and local guidelines and treated confidentially, and all data will be analysed separately for each country and compared across countries. Findings will be disseminated in peer-reviewed scientific journals, national and international conferences, and in briefings to inform clinical decision-making.