Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of a highly saturated genetic map and identification of quantitative trait loci for leaf traits in jujube

Chinese jujube (Ziziphus jujuba Mill.), a member of the genus Ziziphus, which comes under the family Rhamnaceae, is the most important species in terms of its economic, ecological, and social benefits. To dissect the loci associated with important phenotypical traits and analyze their genetic and genomic information in jujube, a whole-genome resequencing (WGR) based highly saturated genetic map was constructed using an F1 hybrid population of 140 progeny individuals derived from the cross of ‘JMS2’ × ‘Jiaocheng 5’. The average sequencing depth of the parents was 14.09× and that of the progeny was 2.62×, and the average comparison efficiency between the sample and the reference genome was 97.09%. Three sets of genetic maps were constructed for a female parent, a male parent, and integrated. A total of 8,684 markers, including 8,158 SNP and 526 InDel markers, were evenly distributed across all 12 linkage groups (LGs) in the integrated map, spanning 1,713.22 cM with an average marker interval of 0.2 cM. In terms of marker number and density, this is the most saturated genetic map of jujube to date, nearly doubling that of the best ones previously reported. Based on this genetic map and phenotype data from 2019 to 2021, 31 leaf trait QTLs were identified in the linkage groups (LG1, 15; LG3, 1; LG5, 8; LG7, 4; LG8, 1, and LG11, 2), including 17 major QTLs. There were 4, 8, 14, and 5 QTLs that contributed to leaf length, leaf width, leaf shape index, and leaf area, respectively. Six QTLs clusters were detected on LG1 (8.05 cM–9.52 cM; 13.12 cM–13.99 cM; 123.84 cM–126.09 cM), LG5 (50.58 cM–50.86 cM; 80.10 cM–81.76 cM) and LG11 (35.98 cM–48.62 cM). Eight candidate genes were identified within the QTLs cluster regions. Annotation information showed that 4 genes (LOC107418196, LOC107418241, LOC107417968, and LOC112492570) in these QTLs are related to cell division and cell wall integrity. This research will provide a valuable tool for further QTL analysis, candidate gene identification, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in jujube.
Comparing coronavirus (COVID-19) and climate change perceptions: Implications for support for individual and collective-level policies

COVID-19 (coronavirus) and climate change are both global issues that have wide-reaching and serious consequences for human health, the economy, and social outcomes for populations around the world, and both require a combination of systemic governmental policies and community support for action. This paper compares people’s responses to the coronavirus pandemic and climate change in the United Kingdom (UK). A representative survey of the UK population (n = 1,518) conducted in November and December 2020 explored public perceptions of (a) personal and government responsibility, (b) efficacy and trust, and (c) support for policies to address the two issues. The results show that, while there are a number of similarities between coronavirus and climate change, major differences exist regarding individual action. In comparison to the coronavirus pandemic, people feel less personal responsibility, think that their own personal actions are less efficacious, and express lower levels of support for (in particular individual-level) policies to address climate change. These findings suggest that experiences from the coronavirus pandemic cannot directly be translated to climate change, and thus that climate change is likely to require different policy responses and framing.
The squeaky wheel gets the grease: Violent civil unrest and global social assistance provision

What are the contemporary determinates of social assistance provision? What is the role of contentious politics? Social assistance literature is dominated by economic and demographic accounts, which under-examine the possibility that governments extend social assistance to contain social unrest. We test factors associated with these “structuralist” and “political” theories on a new panel dataset which includes 54 OECD and emerging market countries between 2002 and 2015. The results indicate social assistance coverage has a significant positive relationship with riots. We explain this outcome as policymakers expanding social assistance as a means of containing violent civil unrest. This effect is more significant in emerging markets, suggesting that the domination of structural explanations is a result of sample bias toward the OECD. Finally, we find that governments consider World Bank social policy recommendations only insofar as there is violent unrest.
Body mass index and quality of life in individuals with polycystic ovary syndrome: Dysmorphic concerns and eating disorders as mediators

Objective Weight issues, dysmorphic concerns and eating disorders are common among individuals with polycystic ovary syndrome (PCOS) and are linked to poor quality of life (QoL). The goal of the current study was to examine whether the association between body mass index (BMI) and QoL was mediated by dysmorphic concerns, examining also the relations with eating disorder symptomatology. Methods Questionnaires were administered to 435 individuals with PCOS aged between 18 and 40 years (M = 27.62; SD = 4.83) to measure dysmorphic concerns, eating disorder symptoms and QoL. Participants were also asked to report their height and weight to compute their BMI. Results Structural equation modeling was used to observe the relationship between the variables. The results revealed a direct relationship between QoL, BMI, dysmorphic concerns and eating disorder symptomatology. In addition, dysmorphic concerns were related to BMI and eating disorder symptomatology. Furthermore, the results showed the mediating role of dysmorphic concerns and eating disorder symptoms in the relationship between BMI and QoL. Conclusion The current results highlight the potential importance of harmful relationships with one's own body and food, explaining why weight issues may be linked to different levels of QoL in PCOS individuals. The implications of these findings are discussed.
Phosphorus mobilization and delivery estimated from long-term high frequency water quality and discharge data

Efficient and targeted measures to mitigate nutrient losses to water are required to meet the challenges of increased food production and climate change. Diffuse pollution management requires insight into the underlying processes of nutrient transfer and its stability, but there are no standardized ways to evaluate phosphorus (P) mobilization and delivery at the catchments scale. Here we suggest a method that allows to systematically and objectively describe catchment scale processes of P transfer to water. Ten years of sub-hourly P concentration and hydrometric data from six agricultural catchments, with different physical characteristics, were assessed to introduce a method for estimation of a P mobilization index and a P delivery index. The former was defined as P detachment/solubilization expressed as ratios of P concentration percentiles, and the latter as connectivity/retention expressed as ratios of P mass load percentiles. Estimating these indices over several years provided insights on the stability of transfer processes over time and the identification of inter-annual trends. The indices were also used to quantify components of the P transfer continuum. This was used as a screening tool to compare and classify catchment specific and potential P loss risks. While the groundwater driven catchments had a higher P mobilization index for reactive P, the hydrologically flashy catchments had higher delivery indices for total P and particulate P + total organic P. Increasing or decreasing inter-annual trends were mostly found in catchments with a chemo-dynamic response in the discharge-concentration relationship. In three catchments the environmental quality standards were frequently exceeded caused by different risks and the P loss screening tool identified the type of risk. Development of the P mobilization and delivery indices was possible with long-term and high frequency monitoring of water quality and discharge from catchments of different typologies, together with a conceptual understanding of the catchments. More catchments of different typologies, management, scales and from different climatic zones are needed for further development of the indices.
Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions

Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap’s integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.
Variational study of Fermi surface deformations in Hubbard models

We study the correlation-induced deformation of Fermi surfaces by means of a new diagrammatic method which allows for the analytical evaluation of Gutzwiller wave functions in finite dimensions. In agreement with renormalization group results we find Pomeranchuk instabilities in two-dimensional Hubbard models for sufficiently large Coulomb interactions.
Exploiting the drought tolerance of wild Elymus species for bread wheat improvement

Crop wild resources are excellent sources of new genetic variation for resilience against climate extremes. However, detailed characterization of the desirable phenotypes is essential before using these crop wild resources in breeding programs. This current study was, therefore, conducted to investigate the water stress responses of eight wild Elymus species and two wheat cultivars. The experiment was carried out under varying levels of osmotic stress induced by polyethylene glycol and progressive water stress through different field capacities. Water stress significantly reduced both physiological and biochemical traits compared to control, ranging from 7.1% (protein content) to 34.5% (chlorophyll) under moderate stress and 9.1–45.8% under severe stress. The anatomical features were also affected under progressive water stress, including a reduction in xylem vessel diameter (7.92 and 16.50%), phloem length (4.36 and 7.18%), vascular bundle length (3.09 and 6.04%), and ground tissue thickness (2.36 and 5.52%), respectively. Conclusively, Elymus borianus (endemic to Swat, Pakistan), E. russelli, E. caninus, E. longioristatus, and E. dauhuricus outperformed the check wheat cultivar, Pirsabak 2005, which is a rainfed variety. The results revealed that Elymus species belonging to the tertiary gene pool of bread wheat could be an excellent drought tolerance source for use in a breeding program.
School staff wellbeing: A network-based assessment of burnout

Burnout is commonly associated with professions that entail a high rate of close relationships with other individuals or groups. This paper explores the association between burnout and interpersonal relationships using a relational, social network framework. We collected data on advice-seeking relationships among 102 teachers and administrative staff from a secondary school in Melbourne, Australia. Burnout was measured using the Burnout Assessment Tool and we focused on four core subscales: (1) exhaustion; (2) mental distance; (3) emotional impairment; and (4) cognitive impairment. We applied a particular class of statistical model for social networks called Exponential Random Graph Models (ERGMs) to shed new light on how level of burnout relates to formation of advice relations among school staff. Results indicated that high levels of overall burnout were linked to a higher number of advice-seeking ties among school staff. Additionally, teachers who scored high in cognitive impairment (i.e., difficulties in thinking clearly and learn new things at work) tended to seek and to provide advice to a greater number of others. Finally, school staff who scored high in exhaustion (i.e., a severe loss of energy that results in feelings of both physical and mental exhaustion) tended to be sought out less as advisors to others, while those high in mental distance (i.e., psychologically distancing oneself from others) were generally less likely to seek advice from other school staff. We discuss these findings drawing on Conservation of Resource theory. Notably, our results show that burnout is not only an individual-level problem, but that burnout is associated with reduced social connectivity in specific ways that may impact on how other school staff collaborate, culminating in a staff-wide overall impact that affects how schools function.
Absolute quantification and characterization of oxylipins in lupus nephritis and systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with multi-organ inflammation and defect, which is linked to many molecule mediators. Oxylipins as a class of lipid mediator have not been broadly investigated in SLE. Here, we applied targeted mass spectrometry analysis to screen the alteration of oxylipins in serum of 98 SLE patients and 106 healthy controls. The correlation of oxylipins to lupus nephritis (LN) and SLE disease activity, and the biomarkers for SLE classification, were analyzed. Among 128 oxylipins analyzed, 92 were absolutely quantified and 26 were significantly changed. They were mainly generated from the metabolism of several polyunsaturated fatty acids, including arachidonic acid (AA), linoleic acid (LA), docosahexanoic acid (DHA), eicosapentanoic acid (EPA) and dihomo-γ-linolenic acid (DGLA). Several oxylipins, especially those produced from AA, showed different abundance between patients with and without lupus nephritis (LN). The DGLA metabolic activity and DGLA generated PGE1, were significantly associated with SLE disease activity. Random forest-based machine learning identified a 5-oxylipin combination as potential biomarker for SLE classification with high accuracy. Seven individual oxylipin biomarkers were also identified with good performance in distinguishing SLE patients from healthy controls (individual AUC > 0.7). Interestingly, the biomarkers for differentiating SLE patients from healthy controls are distinct from the oxylipins differentially expressed in LN patients vs. non-LN patients. This study provides possibilities for the understanding of SLE characteristics and the development of new tools for SLE classification.
Ambroxol for the treatment of COVID-19 among hospitalized patients: A multicenter retrospective cohort study

Ambroxol is a commonly used mucolytic agent principally used to treat respiratory diseases, which may have a role as adjunctive therapy for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, but there is lack of evidence about its effectiveness on coronavirus disease-2019 (COVID-19) patients. To study the association between ambroxol use and clinical outcomes among hospitalized patients of COVID-19 infection. We conducted a multicenter retrospective cohort study involving 3,111 patients with confirmed SARS-CoV-2 infection from three hospitals in Wuhan from 19 December 2019 to 15 April 2020, and the primary outcome was in-hospital mortality. COVID-19 patients were classified into ambroxol and non-ambroxol groups based on the administration of ambroxol during hospitalization. Two analyses including propensity score matching (PSM) to obtain a 1:1 balanced cohort and logistic regression were used to control for confounding factors. The average age of 3,111 patients was 57.55 ± 14.93 years old, 127 of them died during hospitalization, and 924 of them used ambroxol. Treatment with ambroxol did not have a significant effect on in-hospital mortality of COVID-19 patients when compared with non-ambroxol in PSM model after adjusting for confounders (8.0% vs. 3.5%, adjusted OR, 1.03 [95% CI, 0.54–1.97], p = 0.936). Adverse events such as nausea/vomiting, headache, and rash were comparable between the two groups. Our results suggest that the use of ambroxol is not significantly associated with in-hospital mortality in COVID-19 patients, which provides evidence for evaluating the effects of ambroxol on COVID-19 patient outcomes and may be helpful for physicians considering medication alternatives for COVID-19 patients.
Smooth cosmological phase transition in the Hořava-Lifshitz gravity

We show that the cosmological phase transition from the first accelerated expansion in the early universe to the second accelerated expansion over the intermediate decelerated expansion is possible in the HL gravity without the ``detailed balance'' condition if the dark scalar energy density is assumed to be negative. Moreover, we obtain various evolutions depending on the scale factor and the expansion rate. Finally, we discuss the existence of the minimum scale in connection with the singularity free condition.
Quantification of urinary total luteinizing hormone immunoreactivity may improve the prediction of ovulation time

Objectives Most of the currently available ovulation prediction kits provide a relatively rough estimation of ovulation time with a short fertility window. This is due to their focus on the maximum probability of conception occurring one day before ovulation, with no follow-up after LH surge until ovulation nor during the subsequent days thereafter. Earlier studies have shown that urine of reproductive age women contains at least 3 different molecular forms of luteinizing hormone (LH); 1) intact LH, 2) LH beta-subunit (LHβ) and a 3) small molecular weight fragment of LHβ, LHβ core fragment (LHβcf). The proportion of these LH forms in urine varies remarkably during the menstrual cycle, particularly in relation to the mid-cycle LH surge. In this exploratory study, we studied the potential implications of determining the periovulatory course of total LH immunoreactivity in urine (U-LH-ir) and intact LH immunoreactivity in serum (S-LH-ir) in the evaluation of the fertility window from a broader aspect with emphasis on the post-surge segment. Methods We determined total U-LH-ir in addition to intact S-LH-ir, follicle-stimulating hormone (FSH), progesterone, and estradiol in 32 consecutive samples collected daily from 10 women at reproductive age. Inference to the non-intact U-LH-ir levels was made by calculating the proportion of total U-LH-ir to intact S-LH-ir. Results Total U-LH-ir increased along with LH surge and remained at statistically significantly higher levels than those in serum for 5 consecutive days after the surge in S-LH-ir. S-LH-ir returned to follicular phase levels immediately on the following day after the LH surge, whereas the same took 7 days for total U-LH-ir. Conclusions The current exploratory study provides preliminary evidence of the fact that U-LH-ir derived from degradation products of LH remains detectable at peak levels from the LH surge until ovulation and further during the early postovulatory period of fecundability. Thus, non-intact (or total) U-LH-ir appears to be a promising marker in the evaluation of the post-surge segment of the fertility window. Future studies are needed to unravel if this method can improve the prediction of ovulation time and higher rates of fecundability in both natural and assisted conception.
Molecular dynamics identifies semi-rigid domains in the PD-1 checkpoint receptor bound to its natural ligand PD-L1

Cells in danger of being erroneously attacked by leucocytes express PD-L1 on their surface. These cells activate PD-1 on attacking leucocytes and send them to death, thus curbing erroneous, autoimmune attack. Unfortunately, cancer cells exploit this mechanism: By expressing PD-L1, they guard themselves against leucocyte attack and thereby evade immune clearance. Checkpoint inhibitors are drugs which re-enable immune clearance of cancer cells by blocking the binding of PD-L1 to PD-1 receptors. It is therefore of utmost interest to investigate these binding mechanisms. We use three 600 ns all-atom molecular dynamics simulations to scrutinize molecular motions of PD-1 with its binding partner, the natural ligand PD-L1. Usually, atomic motion patterns are evaluated against whole molecules as a reference, disregarding that such a reference is a dynamic entity by itself, thus degrading stability of the reference. As a remedy, we identify semi-rigid domains, lending themselves as more stable and reliable reference frames against which even minute differences in molecular motion can be quantified precisely. We propose an unsupervised three-step procedure. In previous work of our group and others, minute differences in motion patterns proved decisive for differences in function. Here, several highly reliable frames of reference are established for future investigations based on molecular motion.
Muscle mass and physical function in patients with bladder cancer—Data from a prematurely terminated prospective cohort study

Background Patients with bladder cancer (BC) have a high prevalence of comorbidity and low adherence to systemic anticancer treatment but it is unknown whether this is associated with sarcopenia. Objective We aimed to investigate if the sarcopenia-defining parameters (muscle strength, muscle mass and physical performance) were associated with reduced adherence to systemic anticancer treatment in patients with BC, and if these muscle domains changed during treatment. Methods Patients >18 years of age with BC referred for chemotherapy or immunotherapy at Department of Oncology, Rigshospitalet, Denmark were eligible for study inclusion. Measurements were performed before treatment initiation and within one week after treatment termination, and consisted of assessments of muscle strength, muscle mass, and physical performance. Data was compared with thresholds outlined by the European Working Group on Sarcopenia in Older Patient's (EWGSOP2) guidelines and a healthy, age-matched Danish cohort. Results Over a period of 29 months, we included 14 patients of whom two completed follow-up measurements. The recruitment rate was <50% of planned due to logistics and Covid-19 related limitations. Consequently, a decision to prematurely terminate the study was made. No patients fulfilled EWGSOP2 criteria for sarcopenia, but the majority had reduction in one or more muscle domains compared to healthy, age-matched individuals. The majority of patients had poor treatment tolerance, leading to dose reductions and postponed treatments. Conclusions In this prematurely terminated study, no patients fulfilled EWGSOP2 criteria for sarcopenia, yet, most patients were affected in one or more muscle domains and the majority had compromised treatment adherence.