Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying a large number of high-yield genes in rice by pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 gene knockout

Significance Finding the genes that control a complex trait is difficult because each gene may have only minor phenotypic effects. Quantitative trait loci mapping and genome-wide association study techniques have been developed for this purpose but are laborious and time-consuming. Here we developed a method combining pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 technology. By sequencing the parents and descendants of IR8, the Green Revolution “miracle rice,” we identified many genes that had been retained in the pedigree by selection for high yield. Knockout and knockdown studies showed that a large proportion of the identified genes are essential or have phenotypic effects related to production. Our approach provides a powerful means for identifying genes involved in a complex trait. Repeated artificial selection of a complex trait facilitates the identification of genes underlying the trait, especially if multiple selected descendant lines are available. Here we developed a pedigree-based approach to identify genes underlying the Green Revolution (GR) phenotype. From a pedigree analysis, we selected 30 cultivars including the “miracle rice” IR8, a GR landmark, its ancestors and descendants, and also other related cultivars for identifying high-yield genes. Through sequencing of these genomes, we identified 28 ancestral chromosomal blocks that were maintained in all the high-yield cultivars under study. In these blocks, we identified six genes of known function, including the GR gene sd1, and 123 loci with genes of unknown function. We randomly selected 57 genes from the 123 loci for knockout or knockdown studies and found that a high proportion of these genes are essential or have phenotypic effects related to rice production. Notably, knockout lines have significant changes in plant height (P < 0.003), a key GR trait, compared with wild-type lines. Some gene knockouts or knockdowns were especially interesting. For example, knockout of Os10g0555100, a putative glucosyltransferase gene, showed both reduced growth and altered panicle architecture. In addition, we found that in some retained chromosome blocks several GR-related genes were clustered, although they have unrelated sequences, suggesting clustering of genes with similar functions. In conclusion, we have identified many high-yield genes in rice. Our method provides a powerful means to identify genes associated with a specific trait.
Introducing Debtgrep: A Tool for Fighting Technical Debt in Base Station Software

One of the biggest challenges in a large software development project is to manage technical debt. For example, if an API is replaced by a newer version and the old one is deprecated, there is a big risk that a substantial technical debt is incurred. The time where two versions of an API can co-exist can be quite long, and in a big organization like Ericsson 4G5G Baseband there can be a big challenge to prevent developers from continuing to use deprecated API's. At Ericsson 4G5G Baseband we invented the tool debtgrep to be incorporated in our Continuous Integration machinery. The tool will prevent any new code to be added using deprecated API's, or other configured keywords. The tool has proven very useful in the development of a new product based on a new software architecture. Debtgrep is used for deprecated API's, enforcing design rules, and enforcing architecture rules. The paper describes the behavior and configuration possibilities of the tool, and how it is used at Ericsson 4G5G Baseband.
Dyslipidaemia and statin use in individuals aged 10 to <40 years in the T1D Exchange clinic registry

For individuals aged 10 to <40 years with type 1 diabetes and dyslipidaemia, US national guidelines recommend consideration of statin therapy based on age, low‐density lipoprotein cholesterol (LDL‐C) level and other cardiovascular risk factors. We evaluated dyslipidaemia prevalence, statin therapy use, and associations between not meeting target LDL‐C [<100 mg/dL (<5.55 mmol/L)] and other cardiovascular disease (CVD) risk factors in individuals aged 10 to <40 years in the T1D Exchange clinic registry. In 7223 participants, statin use was 2% in 10 to <18 year olds, 4% in 18 to <25 year olds, and 21% in 25 to <40 year olds. Individuals not on statin therapy with LDL‐C above target were more likely to have ≥1 additional CVD risk factor(s) than those with LDL‐C in the target range for all age groups (all P < 0.01). While most individuals not on statin therapy had LDL‐C in the target range, those who did not were more likely to have ≥1 additional CVD risk factor(s), and therefore longitudinal study of lipid levels and statin use is needed to see if treatment of dyslipidaemia to target LDL‐C levels may lower the risk of future CVD in individuals aged 10 to <40 years with type 1 diabetes.
Differential and Predictive Value of Galectin-3 and Soluble Suppression of Tumorigenicity-2 (sST2) in Heart Failure with Preserved Ejection Fraction

Background Galectin-3 and soluble suppression of tumorigenicity-2 (sST2) are promising biomarkers of cardiac fibrosis and ventricular remodeling. The purpose of this study was to investigate the diagnostic and predictive value of galectin-3 and sST2 for use in patients who have heart failure with preserved ejection fraction (HFpEF). Material/Methods A total of 217 hospitalized patients with HF and 30 controls from a physical examination center were included. Venous blood was collected for the detection of circulating expression of galectin-3 and sST2. All the included patients were followed up regularly for 1 year (12±1 months). Results The concentrations of galectin-3 and NT-proBNP were substantially higher following decreased ejection fraction (both P=0.000), except for sST2 (P=0.068 vs. control). In ROC analyses, galectin-3 and NT-proBNP distinguished HFpEF from controls with an area under the curve (AUC) of 0.819 (95% CI: 0.75–0.89, P=0.000) and 0.806 (95% CI: 0.66–0.82, P=0.000). In contrast, sST2 obtained a lower AUC of 0.584 (95% CI: 0.49–0.68, P=0.17) compared to galectni-3 and NT-proBNP. After adjustment for clinical factors and NT-proBNP, galectin-3 was strongly correlated with an increased risk of the endpoint events in HFpEF patients, and the hazard ratio per 1 SD increase of the galectin-3 level was 2.33 (95%CI: 1.72–2.94, P=0.009). Conclusions Galectin-3 is superior to sST2 in distinguishing HFpEF from controls and HFrEF.
Healthy Eating among Mexican Immigrants: Migration in Childhood and Time in the United States

Past research on immigrant health frequently finds that the duration of time lived in the United States is associated with the erosion of immigrants’ health advantages. However, the timing of U.S. migration during the life course is rarely explored. We draw from developmental and sociological perspectives to theorize how migration during childhood may be related to healthy eating among adult immigrants from Mexico. We test these ideas with a mechanism-based age-period-cohort model to disentangle age, age at arrival, and duration of residence. Results show that immigrants who arrived during preschool ages (2–5 years) and school ages (6–11 years) have less healthy diets than adult arrivals (25+ years). After accounting for age at arrival, duration of residence is positively related to healthy eating. Overall, the findings highlight the need to focus more research and policy interventions on child immigrants, who may be particularly susceptible to adopting unhealthy American behaviors during sensitive periods of childhood.
A Predictive Government Decision Based on Citizen Opinions: Tools & Results

Research on citizen satisfaction with respect to public policies has significant public and political value. Politicians are generally seeking effective public policies that favourably impacts citizens' satisfaction. Citizen satisfaction index is a plausible mechanism for public policy makers to monitor and evaluate the public policies. While surveys on citizen satisfaction are common among agile and progressive public administration and governments, automating the computation of citizen's' satisfaction is challenging. Given that surveys and evaluations related to citizen satisfaction are retrospective, remedial actions when necessary are always somewhat late. We describe in this poster a predictive analytics framework for citizen satisfaction with respect to public policy based on the previous citizen sentiments past related policies.
The mutual interplay between calcification and coccolithovirus infection

Summary Two prominent characteristics of marine coccolithophores are their secretion of coccoliths and their susceptibility to infection by coccolithoviruses (EhVs), both of which display variation among cells in culture and in natural populations. We examined the impact of calcification on infection by challenging a variety of Emiliania huxleyi strains at different calcification states with EhVs of different virulence. Reduced cellular calcification was associated with increased infection and EhV production, even though calcified cells and associated coccoliths had significantly higher adsorption coefficients than non‐calcified (naked) cells. Sialic acid glycosphingolipids, molecules thought to mediate EhV infection, were generally more abundant in calcified cells and enriched in purified, sorted coccoliths, suggesting a biochemical link between calcification and adsorption rates. In turn, viable EhVs impacted cellular calcification absent of lysis by inducing dramatic shifts in optical side scatter signals and a massive release of detached coccoliths in a subpopulation of cells, which could be triggered by resuspension of healthy, calcified host cells in an EhV‐free, ‘induced media’. Our findings show that calcification is a key component of the E. huxleyi‐EhV arms race and an aspect that is critical both to the modelling of these host–virus interactions in the ocean and interpreting their impact on the global carbon cycle.
In-Process Monitoring of Lack of Fusion in Ultra-Thin Sheets Edge Welding Using Machine Vision

Lack of fusion can often occur during ultra-thin sheets edge welding process, severely destroying joint quality and leading to seal failure. This paper presents a vision-based weld pool monitoring method for detecting a lack of fusion during micro plasma arc welding (MPAW) of ultra-thin sheets edge welds. A passive micro-vision sensor is developed to acquire clear images of the mesoscale weld pool under MPAW conditions, continuously and stably. Then, an image processing algorithm has been proposed to extract the characteristics of weld pool geometry from the acquired images in real time. The relations between the presence of a lack of fusion in edge weld and dynamic changes in weld pool characteristic parameters are investigated. The experimental results indicate that the abrupt changes of extracted weld pool centroid position along the weld length are highly correlated with the occurrences of lack of fusion. By using such weld pool characteristic information, the lack of fusion in MPAW of ultra-thin sheets edge welds can be detected in real time. The proposed in-process monitoring method makes the early warning possible. It also can provide feedback for real-time control and can serve as a basis for intelligent defect identification.
I Thought I Saw "Zorro": An Inattentional Blindness Study.

Objective Inattentional blindness (IB) refers to an observer's failure to notice unexpected stimulus. The aim of this study was to investigate the effects of the priming type (perceptual, conceptual, and no priming) and emotional context (positive, negative, neutral) on IB with behavioral (IB, non-IB) and eye tracking measurements (latency of first fixation, total fixation time, and total fixation count in response to unexpected stimuli). Methods A total of 193 volunteered male university students were invited in the study. Three thematic videos (positive, negative, and neutral) were created to capture the IB. In the first stage, five pictures (a model dressed in different costumes Zorro as an unexpected stimulus, Vendetta, a judge, a doctor, and a worker) were shown to the participants for priming. In the second stage, a distractor task which involved 30 simple arithmetic operations were given. In the third stage, one of the thematic IB videos were shown to the participants, and then they answered the questions about those videos. Participants were assigned randomly to 9 different experimental conditions according to a 3 (Priming Type: Perceptual, Conceptual, No Priming) x 3 (Emotional Context: Positive, Negative, Neutral) factorial design. Finally, behavioral and eye tracking measurements were collected. Results Main and interaction effects of priming type and emotional contexts were not significant in terms of the behavioral measures. In addition, there were no significant differences between types of priming for eye tracking measures. However, there were significant differences between types of emotional contexts in all eye tracking measurements. In the negative context, participants made less total fixation, and looked shorter to unexpected stimulus than positive and neutral contexts. In addition, non-notifiers made less total fixation, and looked at unexpected stimulus for a shorter time compared to notifiers. Conclusion The fact of "looking without seeing" was again demonstrated experimentally. Priming and emotional context did not affect behavioral data, but eye movements were affected from the emotional context. Current findings showed a relation between emotion and attention.
No Effects of Black Tea on Cognitive Decline Among Older US Men: A Prospective Cohort Study.

BACKGROUND Accumulating evidence supports the neuroprotective effects of bioactive compounds from tea leaves. There are limited data from black tea consumption populations. OBJECTIVE To determine whether black tea consumption is associated with cognitive decline among older men. METHODS We chose to study the association between black tea consumption and cognition using data from the Osteoporotic Fractures in Men (MrOS) cohort, which collected information on tea consumption at baseline and has repeatedly assessed cognitive function in 3,844 men aged 65+ years (mean = 72.4 years). We defined tea drinkers as those who drank black tea at least once per week and further grouped them into weekly drinkers and daily drinkers. Cognitive function was assessed at baseline and approximately 7 years later using the Modified Mini-Mental State Examination (3MSE). Multivariable logistic regression and linear regression models were constructed to assess the association between black tea consumption and risk of fast cognitive decline as a binary variable and change in 3MSE scores as continuous variable. Fast cognitive decline was defined as decline in 3MSE >1.5 standard deviation of mean change score. Models were adjusted for age, education level, and baseline cognitive scores. RESULTS Weekly and daily black tea drinkers were 24.8% and 12.4% of the study cohort, respectively. Fast cognitive decline occurred in 243 (6.3%) participants. Tea consumption was not associated with risk of cognitive decline, nor was tea associated with cognitive decline measured by absolute change in 3MSE scores. CONCLUSIONS There was no association of black tea consumption and cognitive decline among older men in the US.
Young Muslim Women Living with Asthma in Denmark: A Link between Religion and Self-Efficacy

Asthma is a chronic respiratory disease that can be controlled with appropriate medicinal treatment. Adherence to pharmacological treatment is therefore critical. Self-efficacy plays a key role in adherence to medicine in chronic diseases, including asthma. Additionally, ethnic minorities have poor adherence to medicines. However, the impact of religion on self-efficacy and adherence is understudied. Therefore, the aim of this study was to explore the role of self-efficacy in adherence to asthma medicine treatment and the influence of religion on self-efficacy among young, Muslim minority women. A focus group and individual interviews with 10 Muslim minority women (14–24 years of age) living in Denmark were conducted. Data analysis was deductive using Bandura’s theory of self-efficacy and modes of agency. Overall, religion was shown to affect self-efficacy. The women reported changes in self-perceived self-efficacy during the holy month of Ramadan. In addition, praying was used as an alternative to medicine for controlling asthma symptoms. However, the women did not perceive religion and treating asthma with medicine as mutually exclusive, but rather as coexisting for the shared goal of controlling asthma symptoms. It is important for healthcare professionals (HCPs) to be aware of the link between self-efficacy, religion and adherence to asthma medicine treatment. This awareness can aid HCPs in giving advice regarding adherence to asthma treatment, and when monitoring treatment to improve the quality of asthma care for young Muslim minority women.
Role of the Nurse Navigator: integrative review.

OBJECTIVE To identify scientific literature on oncology nurses who provide patient navigation services as nurse navigators. METHODS Integrative review of literature searches in the databases LILACS, MEDLINE/PubMed, SCOPUS, SciELO, Web of Science and Science Direct based on the descriptors patient; navigation; nurse; professional; cancer; oncology; navigator; and navigators. RESULTS Seventeen articles were identified and grouped according to the following thematic approach: Care Processes; Patients; and Health Workers. It was observed that scientific literature on nurse navigators mostly comes from the United States, Australia, Canada, Sweden, and Demark, where the first nurse navigator programmes were introduced. No studies were found in local journals or populations. CONCLUSIONS The nurse navigator offer a unique service for the provision of quality care. Although international research is recent, further studies on the role of these professionals are clearly needed.
Fast Feature-Preserving Approach to Carpal Bone Surface Denoising

We present a geometric framework for surface denoising using graph signal processing, which is an emerging field that aims to develop new tools for processing and analyzing graph-structured data. The proposed approach is formulated as a constrained optimization problem whose objective function consists of a fidelity term specified by a noise model and a regularization term associated with prior data. Both terms are weighted by a normalized mesh Laplacian, which is defined in terms of a data-adaptive kernel similarity matrix in conjunction with matrix balancing. Minimizing the objective function reduces it to iteratively solve a sparse system of linear equations via the conjugate gradient method. Extensive experiments on noisy carpal bone surfaces demonstrate the effectiveness of our approach in comparison with existing methods. We perform both qualitative and quantitative comparisons using various evaluation metrics.
Non-linear dynamics of heart rate variability during incremental cycling exercise

ABSTRACT Within the last years complex models of cardiovascular regulation and exercise fatigue have implemented heart rate variability (HRV) as a measure of autonomic nervous system. Using detrended fluctuation analysis (DFA) to assess heart rate correlation properties, the present study examines the influence of exercise intensity on total variability and complexity in non-linear dynamics of HRV. Sixteen cyclists performed a graded exercise test on a bicycle ergometer. HRV time domain measures and fractal correlation properties were analyzed using short-term scaling exponent alpha1 of DFA. Amplitude and complexity of HRV parameters decreased significantly. DFA-alpha1 increased from rest to low exercise intensity and showed an almost linear decrease from higher intensities until exhaustion. These findings support a qualitative change in self-organized heart rate regulation from a complex autonomic control at rest and low intensities towards a breakdown of the interaction in control mechanisms with non-autonomic heart rate control dominating at high intensities.
A Scoping Review of Challenges in Adult Intimate Relationships After Childhood Sexual Abuse

ABSTRACT Childhood sexual abuse is a severe problem worldwide. Childhood sexual abuse can be detrimental to children and their abilities to cope with and communicate in their subsequent adult intimate relationships. The aim of this review was to generate and summarize knowledge about how childhood sexual abuse manifests in adult intimate relationships so healthcare professionals can incorporate this knowledge into treatment and care. A scoping review methodology was selected because it supports examination of the extent, range, and nature of research activity. A content analysis of the studies included in this review led to three thematic categories of challenges in adult intimate relationships after childhood sexual abuse: (a) relationship satisfaction, (b) sexual satisfaction, and (c) communication and trust.
Modification of betanodavirus virulence by substitutions in the 3' terminal region of RNA2

Betanodaviruses have bi-segmented positive-sense RNA genomes, consisting of RNAs 1 and 2. For some members of the related genus alphanodavirus, the 3′ terminal 50 nucleotides (nt) of RNA2, including a predicted stem-loop structure (3′SL), are essential for replication. We investigate the possible existence and role of a similar structure in a reassortant betanodavirus strain (RGNNV/SJNNV). In this study, we developed three recombinant strains containing nucleotide changes at positions 1408 and 1412. Predictive models showed stem-loop structures involving nt 1398–1421 of the natural reassortant whereas this structure is modified in the recombinant viruses harbouring point mutations r1408 and r1408–1412, but not in r1412. Results obtained from infectivity assays showed differences between the reference strains and the mutants in both RNA1 and RNA2 synthesis. Moreover, an imbalance between the synthesis of both segments was demonstrated, mainly with the double mutant. All these results suggest an interaction between RNA1 and the 3′ non-coding regions (3′NCR) of RNA2. In addition, the significant attenuation of the virulence for Senegalese sole and the delayed replication of r1408–1412 in brain tissues may point to an interaction of RNA2 with host cellular proteins.