Miracle-dz/UniFAR-FTUs huggingface dataset:
QTL mapping reveals candidate genes for main agronomic traits in Luffa based on a high-resolution genetic map

Luffa is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated Luffa cultivars, Luffa acutangula and Luffa cylindrica. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC1 population of 110 lines derived from a cross between S1174 (Luffa acutangula) and P93075 (Luffa cylindrica). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (qID2) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. Lac09g006860 (LacCRWN3), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in qID2. Sequence alignment showed completely different promoter sequences between the two parental alleles of LacCRWN3 except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for LacCRWN3: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that LacCRWN3, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of Luffa. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in Luffa.
Ontological and epistemological commitments in interdisciplinary water research: Uncertainty as an entry point for reflexion

Against the background of a renewed interest in interdisciplinary water research, we begin this paper by diagnosing a need for deeper engagement at the epistemological and ontological level. We then analyse the ontological and epistemological commitments of three modeling examples: an academic human-flood model, a nutrient transfer decision support model and a policy facing water security model. These examples demonstrate how research practices are not neutral but intervene in the world by distributing agency unequally, providing naturalized and de-politicized explanations of the past and pre-configuring certain futures while foreclosing others. Lastly, we position hydrology's uncertainty tradition and its problematisation of choices in the research process as an entry point for reflexion on the contingencies of and ethical responsibility for research practices. This uncertainty tradition provides more common ground for collaboration between hydrologists and critical water researchers than previously acknowledged, while such collaboration would still thrive on confrontation. We conclude with a call for greater humility in water research, especially when using models, and practical suggestions for how researchers could uncover ontological and epistemological commitments and live up to the ethical responsibility they entail.
Foxp3+ regulatory T cell therapy for tolerance in autoimmunity and solid organ transplantation

Regulatory T cells (Tregs) are critical for tolerance in humans. The exact mechanisms by which the loss of peripheral tolerance leads to the development of autoimmunity and the specific role Tregs play in allograft tolerance are not fully understood; however, this population of T cells presents a unique opportunity in the development of targeted therapeutics. In this review, we discuss the potential roles of Foxp3+ Tregs in the development of tolerance in transplantation and autoimmunity, and the available data regarding their use as a treatment modality.
Honeybees are buffered against undernourishment during larval stages

The negative impact of juvenile undernourishment on adult behavior has been well reported for vertebrates, but relatively little is known about invertebrates. In honeybees, nutrition has long been known to affect task performance and timing of behavioral transitions. Whether and how a dietary restriction during larval development affects the task performance of adult honeybees is largely unknown. We raised honeybees in-vitro, varying the amount of a standardized diet (150 µl, 160 µl, 180 µl in total). Emerging adults were marked and inserted into established colonies. Behavioral performance of nurse bees and foragers was investigated and physiological factors known to be involved in the regulation of social organization were quantified. Surprisingly, adult honeybees raised under different feeding regimes did not differ in any of the behaviors observed. No differences were observed in physiological parameters apart from weight. Honeybees were lighter when undernourished (150 µl), while they were heavier under the overfed treatment (180 µl) compared to the control group raised under a normal diet (160 µl). These data suggest that dietary restrictions during larval development do not affect task performance or physiology in this social insect despite producing clear effects on adult weight. We speculate that possible effects of larval undernourishment might be compensated during the early period of adult life.
Relationship between Tropospheric Circulation over the Western North Pacific and Tropical Cyclone Approach/Landfall on Japan

The relationship between large-scale seasonal (June-October) circulation over the western North Pacific, and the frequency of tropical cyclone (TC) approach or landfall on Japan, is examined using the reanalysis datasets (ERA-40(1958-2001) and JRA-25(1979-2004)). The result shows that there are two dominant modes over the western North Pacific; the El Nino Southern Oscillation (ENSO) mode, and a mode that is correlated with the variation of the subtropical high. In years when the subtropical high extends westward from its climatological position and the maximum of the high pressure anomaly is located along the Tropic of Cancer, the frequency of TC approach/landfall on Japan tends to be reduced. In contrary, when the subtropical high retreats eastward, and the maximum of low pressure anomaly is located along the Tropic of Cancer, there is a tendency to have more number of tropical cyclones approach or landfall on Japan.
Effects of cysteine addition to low-fishmeal diets on the growth, anti-oxidative stress, intestine immunity, and Streptococcus agalactiae resistance in juvenile golden pompano (Trachinotus ovatus)

As the precursor of taurine, cysteine serves physiological functions, such as anti-oxidative stress and immune improvement. Investigation of cysteine and its derivatives has made positive progress in avian and mammalian species, yet the study and application of cysteine in aquatic animals are relatively rare. Therefore, we evaluated the effects of supplementing a low-fishmeal diet with various levels of cysteine on the growth, antioxidant capacity, intestine immunity, and resistance against Streptococcus agalactiae of the juvenile golden pompano (Trachinotus ovatus). According to our study, exogenous supplementation with 0.6-1.2% cysteine greatly increased the final body weight (FBW) and specific growth rate (SGR) of golden pompano compared to the control group. Under the present conditions, the optimum dietary cysteine supplementation level for golden pompano was 0.91% based on the polynomial regression analysis of SGR. Meanwhile, we found that the Nrf2/Keap1/HO-1 signaling pathway was notably upregulated with the increase of exogenous cysteine, which increased antioxidant enzyme activity in serum and gene expression in the intestine and reduced the level of reactive oxygen species (ROS) in the serum of golden pompano. In addition, morphological analysis of the midgut demonstrated that exogenous cysteine improved muscle thickness and villi length, which suggested that the physical barrier of the intestine was greatly strengthened by cysteine. Moreover, cysteine increased the diversity and relative abundance of the intestinal flora of golden pompano. Cysteine suppressed intestinal NF-κB/IKK/IκB signaling and pro-inflammatory cytokine mRNA levels. Conversely, intestinal anti-inflammatory cytokine gene expression and serum immune parameters were upregulated with the supplementary volume of cysteine and improved intestine immunity. Further, exogenous cysteine supplementation greatly reduced the mortality rate of golden pompano challenged with S. agalactiae. In general, our findings provide more valuable information and new insights into the rational use of cysteine in the culture of healthy aquatic animals.
Cell-based therapy in prophylaxis and treatment of chronic graft-versus-host disease

Hematopoietic allogeneic stem cell transplantation (allo-SCT) is a curative option for patients with hematological malignancies. However, due to disparities in major and minor histocompatibility antigens between donor and recipient, severe inflammatory complications can occur, among which chronic graft-versus-host disease (cGVHD) can be life-threatening. A classical therapeutic approach to the prevention and treatment of cGVHD has been broad immunosuppression, but more recently adjuvant immunotherapies have been tested. This review summarizes and discusses immunomodulatory approaches with T cells, including chimeric antigen receptor (CAR) and regulatory T cells, with natural killer (NK) cells and innate lymphoid cells (ILCs), and finally with mesenchymal stromal cells (MSC) and extracellular vesicles thereof. Clinical studies and pre-clinical research results are presented likewise.
Phenotypic convergence of bacterial adaption to sub-lethal antibiotic treatment

Microorganisms can adapt quickly to changes in their environment, leading to various phenotypes. The dynamic for phenotypic plasticity caused by environmental variations has not yet been fully investigated. In this study, we analyzed the time-series of phenotypic changes in Staphylococcus cells during adaptive process to antibiotics stresses using flow cytometry and Raman spectroscopy. The nine antibiotics with four different mode of actions were treated in bacterial cells at a sub-lethal concentration to give adaptable stress. Although the growth rate initially varied depending on the type of antibiotic, most samples reached the maximum growth comparable to the control through the short-term adaptation after 24 h. The phenotypic diversity, which showed remarkable changes depending on antibiotic treatment, converged identical to the control over time. In addition, the phenotype with cellular biomolecules converted into a bacterial cell that enhance tolerance to antibiotic stress with increases in cytochrome and lipid. Our findings demonstrated that the convergence into the phenotypes that enhance antibiotic tolerance in a short period when treated with sub-lethal concentrations, and highlight the feasibility of phenotypic approaches in the advanced antibiotic treatment.
Epidemiology of compassion: A literature review

Psychology and neuroscience have contributed significantly to advances in understanding compassion. In contrast, little attention has been given to the epidemiology of compassion. The human experience of compassion is heterogeneous with respect to time, place, and person. Therefore, compassion has an epidemiology, although little is known about the factors that account for spatial or temporal clustering of compassion or how these factors might be harnessed to promote and realize a more compassionate world. We reviewed the scientific literature to describe what is known about “risk factors” for compassion towards others. Studies were included if they used quantitative methods, treated compassion as an outcome, and used measures of compassion that included elements of empathy and action to alleviate suffering. Eighty-two studies met the inclusion criteria; 89 potential risk factors were tested 418 times for association with compassion. Significant associations with compassion were found for individual demographic factors (e.g., gender, religious faith); personal characteristics (e.g., emotional intelligence, perspective-taking, secure attachment); personal experience (e.g., previous adversity); behaviors (e.g., church attendance); circumstantial factors during the compassion encounter (e.g., perceptions of suffering severity, relational proximity of the compassion-giver and -receiver, emotional state of the compassion-giver); and organizational features. Few studies explored the capacity to receive, rather than give, compassion. Definitions and measures of compassion varied widely across disciplines; 87% of studies used self-report measures and 39% used a cross-sectional design. Ten randomized clinical trials documented the effectiveness of compassion training. From an epidemiologic perspective, most studies treated compassion as an individual host factor rather than as transmissible or influenced by time or the environment. The causal pathways leading from suffering to a compassionate response appear to be non-linear and complex. A variety of factors (acting as effect modifiers) appear to be permissive of—or essential for—the arising of compassion in certain settings or specific populations. Future epidemiologic research on compassion should take into account contextual and environmental factors and should elucidate compassion-related dynamics within organizations and human systems. Such research should be informed by a range of epidemiologic tools and methods, as well as insights from other scientific disciplines and spiritual and religious traditions.
Divergent dynamics of inflammatory mediators and multiplex PCRs during airway infection in cystic fibrosis patients and healthy controls: Serial upper airway sampling by nasal lavage

Background In cystic fibrosis (CF), acute respiratory exacerbations critically enhance pulmonary destruction. Since these mainly occur outside regular appointments, they remain unexplored. We previously elaborated a protocol for home-based upper airway (UAW) sampling obtaining nasal-lavage fluid (NLF), which, in contrast to sputum, does not require immediate processing. The aim of this study was to compare UAW inflammation and pathogen colonization during stable phases and exacerbations in CF patients and healthy controls. Methods Initially, we obtained NLF by rinsing 10 ml of isotonic saline/nostril during stable phases. During exacerbations, subjects regularly collected NLF at home. CF patients directly submitted one aliquot for microbiological cultures. The remaining samples were immediately frozen until transfer on ice to our clinic, where PCR analyses were performed and interleukin (IL)-1β/IL-6/IL-8, neutrophil elastase (NE), matrix metalloproteinase (MMP)-9, and tissue inhibitor of metalloproteinase (TIMP)-1 were assessed. Results Altogether, 49 CF patients and 38 healthy controls (HCs) completed the study, and 214 NLF samples were analyzed. Of the 49 CF patients, 20 were at least intermittently colonized with P. aeruginosa and received azithromycin and/or inhaled antibiotics as standard therapy. At baseline, IL-6 and IL-8 tended to be elevated in CF compared to controls. During infection, inflammatory mediators increased in both cohorts, reaching significance only for IL-6 in controls (p=0.047). Inflammatory responses tended to be higher in controls [1.6-fold (NE) to 4.4-fold (MMP-9)], while in CF, mediators increased only moderately [1.2-1.5-fold (IL-6/IL-8/NE/TIMP-1/MMP-9)]. Patients receiving inhalative antibiotics or azithromycin (n=20 and n=15, respectively) revealed lower levels of IL-1β/IL-6/IL-8 and NE during exacerbation compared to CF patients not receiving those antibiotics. In addition, CF patients receiving azithromycin showed MMP-9 levels significantly lower than CF patients not receiving azithromycin at stable phase and exacerbation. Altogether, rhinoviruses were the most frequently detected virus, detected at least once in n=24 (49.0%) of the 49 included pwCF and in n=26 (68.4%) of the 38 healthy controls over the 13-month duration of the study. Remarkably, during exacerbation, rhinovirus detection rates were significantly higher in the HC group compared to those in CF patients (65.8% vs. 22.4%; p<0.0001). Conclusion Non-invasive and partially home-based UAW sampling opens new windows for the assessment of inflammation and pathogen colonization in the unified airway system.
A cohort study of circulating progenitor cells after ST-segment elevation and non-ST segment elevation myocardial infarction in non-diabetic and diabetic patients

Background Myocardial infarction induces elevation of progenitor cells in the circulation, a reparative response inhibited by type-2 diabetes. Objectives Determine if myocardial infarct severity and diabetes interactively influence the migratory activity of CD34+/CXCR4+ progenitor cells and if the migratory test predicts cardiac outcomes. Materials and methods A longitudinal study was conducted on patients with or without diabetes with a STEMI or NSTEMI. CD34+/CXCR4+ cells were measured in the peripheral blood using flow cytometry, and migratory activity was tested in vitro on cells isolated from samples collected on days 0 and 4 post-infarct. Cardiac function was assessed at three months using cardiac MRI. Results Of 1,149 patients screened, 71 (6.3%) were eligible and consented. Fifty had STEMI (16 with diabetes) and 21 NSTEMI (8 with diabetes). The proportion of CD34+/CXCR4+ cells within blood mononuclear cells was 1.96 times higher after STEMI compared with NSTEMI (GMR = 1.96, 95% CI 0.87, 4.37) and 1.55 times higher in patients with diabetes compared to patients without diabetes (GMR = 1.55, 95% CI 0.77, 3.13). In the latter, STEMI was associated with a 2.42-times higher proportion of migrated CD34 + /CXCR4 + cells compared with NSTEMI (GMR = 2.42, 95% CI 0.66, 8.81). In patients with diabetes, the association was the opposite, with a 55% reduction in the proportion of migrated CD34+/CXCR4+ cells. No statistically significant associations were observed between the frequency in peripheral blood or in vitro migration capacity of CD34+/CXCR4+ cells and MRI outcomes. Conclusion We document the interaction between infarct and diabetes on the migratory activity of CD34+/CXCR4+ cells. The test did not predict functional outcomes in the studied cohort.
Unraveling the effect of the combination of modified atmosphere packaging and ε-polylysine on the physicochemical properties and bacterial community of greater amberjack (Seriola dumerili)

The combined effect of ε-polylysine (PL) and modified atmosphere packaging (MAP; 60% CO2/40% N2) on the bacterial community of greater amberjack filets and their physicochemical properties was evaluated at 4°C. The total viable counts (TVC), psychrotrophic bacterial count, sensory index, texture analysis, and total volatile basic nitrogen (TVB-N) revealed that PL, MAP, and MAP + PL treatment delayed the deterioration of greater amberjack filets. These treatment groups also showed decreased accumulation of biogenic amines. High-throughput 16S rRNA gene sequencing results indicated that these treatments suppressed the growth of Pseudomonas in greater amberjack filets. Furthermore, the MAP + PL treatment group was observed to be more effective than the PL and MAP groups, extending the shelf life of greater amberjack filets by 6 days. This investigation showed that the combination of PL and MAP has the potential to retain the quality and extend the shelf life of greater amberjack.
Detection and management of postpartum haemorrhage: Qualitative evidence on healthcare providers' knowledge and practices in Kenya, Nigeria, and South Africa

Background Postpartum haemorrhage (PPH) is the leading cause of maternal death globally. Most PPH deaths can be avoided with timely detection and management; however, critical challenges persist. A multi-country cluster-randomised trial (E-MOTIVE) will introduce a clinical care bundle for early detection and first-response PPH management in hospital settings. This formative qualitative study aimed to explore healthcare providers' knowledge and practices of PPH detection and management after vaginal birth, to inform design and implementation of E-MOTIVE. Methods Between July 2020–June 2021, semi-structured qualitative interviews were conducted with 45 maternity healthcare providers (midwives, nurses, doctors, managers) of nine hospitals in Kenya, Nigeria, and South Africa. A thematic analysis approach was used. Results Four key themes were identified, which varied across contexts: in-service training on emergency obstetric care; limited knowledge about PPH; current approaches to PPH detection; and current PPH management and associated challenges. PPH was recognised as an emergency but understanding of PPH varied. Early PPH detection was limited by the subjective nature of visual estimation of blood loss. Lack of expertise on PPH detection and using visual estimation can result in delays in initiation of PPH management. Shortages of trained staff and essential resources, and late inter-hospital referrals were common barriers to PPH management. Conclusion There are critical needs to address context-specific barriers to early and timely detection and management of PPH in hospital settings. These findings will be used to develop evidence-informed implementation strategies, such as improved in-service training, and objective measurement of blood loss, which are key components of the E-MOTIVE trial (Trial registration: ClinicalTrials.gov: NCT04341662).
Cosmic-ray spallative origin of the rare odd-odd nuclei, consistent with light-element production

Reeves, Fowler, and Hoyle have suggested that the light nuclei could be synthesized by mutual spallation of the cosmic rays and the interstellar medium. Preliminary work by Audouze showed that the rare odd-odd nuclides /sup 50/V and /sup 180/Ta might also be produced by this process. An integral is performed over all cosmic-ray energies, utilize the newly avilable more accurate cross sections for peripheral reactions are utilized, and consider the effect of large fluxes of low-energy (5--25 MeV) particles in the region where (p,n) cross sections are very high is considered, to show that one might be able in some specific models to produce not only additional /sup 7/Li and /sup 11/B, which are not fitted well in standard models, but also some additional /sup 138/La, thus possibly filling in a gap in those models by adding that nuclide to the other rare odd-odd nuclides /sup 50/V and /sup 180/Ta produced by spallation at higher energies. (AIP)