Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction

ABSTRACT The thickening of plant organs is supported by secondary growth, a process by which new vascular tissues (xylem and phloem) are produced. Xylem is composed of several cell types, including xylary fibers, parenchyma and vessel elements. In Arabidopsis, it has been shown that fibers are promoted by the class-I KNOX gene KNAT1 and the plant hormones gibberellins, and are repressed by a small set of receptor-like kinases; however, we lack a mechanistic framework to integrate their relative contributions. Here, we show that DELLAs, negative elements of the gibberellin signaling pathway, physically interact with KNAT1 and impair its binding to KNAT1-binding sites. Our analysis also indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall modifications and phenylpropanoid biosynthesis. Moreover, the promotion by constitutive overexpression of KNAT1 of fiber formation and the expression of genes required for fiber differentiation were still reverted by DELLA accumulation, in agreement with post-translational regulation of KNAT1 by DELLA proteins. These results suggest that gibberellins enhance fiber development by promoting KNAT1 activity. Summary: KNAT1-overexpressing Arabidopsis mutants reveal that gibberellin signaling promotes xylem fiber development by preventing DELLA-dependent inhibition of KNAT1 activity.
Italy and a Needed Public Investment Boost: The Demand and the Supply Side

The controversial nature of public investment as a countercyclical demand stimulus has contributed to obscure the issue of its long term fall, with many governments feeling justified in making deeper cuts for public investment expenditure during both phases of the economic cycle, and many others favoring public-private partnerships and other forms of blended financing. In addition to the overall fall, an asset substitution process has progressively reduced the truly social part of public investment, which in developing and developed countries alike may be well below the mark of 1-2% of GDP. This negative trend is made more dramatic by the fact that virtually the only public investment with a reach beyond the single countries is of public- private nature and thus explicitly excludes multilateral assets of pure public good nature, such as intercountry infrastructure and multilateral social welfare programs. The situation is especially dramatic for Italy, where the fall of public investment has contributed to the decline of key components of the country human and social capital endowment. This article explores some of the most important dimensions of this phenomenon, concentrating on the supply rather than the demand side effects, and proposes a solution based on a conditioned expansion of European public investment, concentrated in highly productive assets such as education and infrastructure.
Comparing women’s financial costs of induced abortion at a facility vs. seeking treatment for complications from unsafe abortion in Zambia

Abstract Although abortion is legal in Zambia under a variety of broad conditions, unsafe abortion remains common. The purpose of this project was to compare the financial costs for women when they have an induced abortion at a facility, with costs for an induced abortion outside a facility, followed by care for abortion-related complications. We gathered household wealth data at one point in time (T1) and longitudinal qualitative data at two points in time (T1 and T2, three-four months later), in Lusaka and Kafue districts, between 2014 and 2015. The data were collected from women (n = 38) obtaining a legal termination of pregnancy (TOP), or care for unsafe abortions (CUA). The women were recruited from four health facilities (two hospitals and two private clinics, one of each per district). At T2, CUA cost women, on average, 520 ZMW (USD 81), while TOP cost women, on average, 396 ZMW (USD 62). About two-thirds of the costs had been incurred by T1, while an additional one-third of the total costs was incurred between T1 and T2. Women in all three wealth tertiles sought a TOP in a health facility or an unsafe abortion outside a facility. Women who obtained CUA tended to be further removed from the money that was used to pay for their abortion care. Women’s financial dependence leaves them unequipped to manage a financial shock such as an abortion. Improved TOP and post-abortion care are needed to reduce the health sequelae women experience after both types of abortion-related care.
Anterior placenta previa in the mid-trimester of pregnancy as a risk factor for neonatal respiratory distress syndrome

This study investigated whether anterior placenta previa in the second trimester is associated with neonatal respiratory distress syndrome (RDS). The neonates delivered by 2067 women between 2007 and 2015 were evaluated for the presence of RDS through birth records. The location of the placenta and the presence of placenta previa during the second and third trimesters were assessed and recorded. Demographic, prenatal, and perinatal records were reviewed. Anterior placenta previa in the second and third trimesters was correlated with RDS. Infants with lower gestational ages and birth weights had higher rates of RDS. Multivariate logistic regression analysis identified a significant association between anterior placenta previa in the second trimester and neonatal RDS. Anterior placenta previa in the second trimester is associated with neonatal RDS. Obstetricians should be aware that anterior placenta previa detected during the second trimester, irrespective of whether the placenta will migrate in the third trimester, may be an independent risk factor for neonatal RDS.
Chemical and Non-Chemical Options for Managing Twospotted Spider Mite, Western Tarnished Plant Bug and Other Arthropod Pests in Strawberries

California strawberries have two major arthropod pests—the twospotted spider mite, Tetranychus urticae and the western tarnished plant bug, Lygus hesperus, which result in significant losses to the yield and quality of marketable berries. Other important insect pests that are frequently seen in strawberry include the greenhouse whitefly, Trialeurodes vaporariorum and the western flower thrips, Frankliniella occidentalis that cause varying levels of damage depending on the level of infestation. Chemical pesticides play a major role in managing these pests but not without the associated risk of pesticide resistance and environmental safety. Two field studies were conducted in commercial strawberry fields in Santa Maria, one of the strawberry growing areas in California Central Coast, to determine the efficacy of chemical, botanical and microbial pesticides in the integrated pest management (IPM) of strawberry. Chemical, botanical and microbial pesticides were evaluated against T. urticae in a small plot study in 2013 and against L. hesperus and other insect pests in a large plot study in 2015 in commercial strawberry fields. Bug vacuums were also used in the 2015 study. Results demonstrated that non-chemical alternatives can play an important role in strawberry IPM.
Inflammation and vascular permeability correlate with growth in sporadic vestibular schwannoma

Abstract Background Inflammation is hypothesized to be a key event in the growth of sporadic vestibular schwannoma (VS). In this study we sought to investigate the relationship between inflammation and tumor growth in vivo using the PET tracer 11C-(R)-PK11195 and dynamic contrast enhanced (DCE) MRI derived vascular biomarkers. Methods Nineteen patients with sporadic VS (8 static, 7 growing, and 4 shrinking tumors) underwent prospective imaging with dynamic 11C-(R)-PK11195 PET and a comprehensive MR protocol, including high temporal resolution DCE-MRI in 15 patients. An intertumor comparison of 11C-(R)-PK11195 binding potential (BPND) and DCE-MRI derived vascular biomarkers (Ktrans, vp, ve) across the 3 different tumor growth cohorts was undertaken. Tissue of 8 tumors was examined with immunohistochemistry markers for inflammation (Iba1), neoplastic cells (S-100 protein), vessels (CD31), the PK11195 target translocator protein (TSPO), fibrinogen for vascular permeability, and proliferation (Ki-67). Results were correlated with PET and DCE-MRI data. Results Compared with static tumors, growing VS displayed significantly higher mean 11C-(R)-PK11195 BPND (−0.07 vs 0.47, P = 0.020), and higher mean tumor Ktrans (0.06 vs 0.14, P = 0.004). Immunohistochemistry confirmed the imaging findings and demonstrated that TSPO is predominantly expressed in macrophages. Within growing VS, macrophages rather than tumor cells accounted for the majority of proliferating cells. Conclusion We present the first in vivo imaging evidence of increased inflammation within growing sporadic VS. Our results demonstrate that 11C-(R)-PK11195 specific binding and DCE-MRI derived parameters can be used as imaging biomarkers of inflammation and vascular permeability in this tumor group.
Intubation, tracheostomy, and decannulation in patients with Guillain–Barré–syndrome—does dysphagia matter?

Introduction: Although patients with Guillain–Barré syndrome frequently require orotracheal intubation and tracheostomy, the incidence and relevance of neurogenic dysphagia prior to intubation and risk factors for prolonged requirement for a tracheal cannula have not yet been identified. Methods: Retrospective analysis of the medical records of 88 patients was performed. Clinical characteristics were compared between intubated and nonintubated patients and between immediately decannulated and not immediately decannulated patients. Results: Thirty‐five (39.7%) patients required tracheostomy. Neuromuscular weakness and related respiratory insufficiency were the main reasons for intubation. In the subgroup of tracheotomized patients, immediate decannulation after completed respiratory weaning was possible in 14 (40%) patients. The severity of dysphagia, in particular pharyngolaryngeal hypesthesia, was related to the length of cannulation. Discussion: Respiratory muscle weakness is the main reason for intubation, whereas neurogenic dysphagia is the main risk factor for persisting cannulation. Dysphagia after weaning is most frequently characterized by severe laryngeal sensory deficit. Muscle Nerve 59:194–200, 2019
Biological Age Is Associated with the Active Use of Nutrition Data

Purpose Biological age (BA) has recently emerged as a substitute for chronological age (CA), and many subjects seek to optimally control their BA. However, in South Korea, no study has adequately explored factors that affect BA, although individual health management is essential to preventing chronic diseases. In the present study, we focus on the use of health information, in particular nutrition facts, to control BA. Methods We used data from the Korea National Health and Nutrition Examination Surveys (2010–2015; 26,914 eligible participants) using BA and age differences as outcome variables. We used multiple linear regression to explore the relationship between the use of nutrition data and differences in BA after adjusting for covariates. In addition, we used multiple linear regression to examine subgroup differences in such relationships. Results 12.8% of males and 27.5% of females used nutrition facts when deciding which foods to purchase. The more attention paid to such facts, the lower the BA and BA differences in both males and females (males: β = −2.646, females: β = −2.787, p < 0.05, for BA; males: β = −1.181, females, β = −2.161, p < 0.05, for BA differences). However, BA differences were more significant in subjects with chronic disease, obesity, and/or a family history of chronic disease. Conclusion High-level awareness of and active use of nutrition facts permitted effective self-management in preventing chronic disease and improving BA, particularly in subjects at higher risk for chronic disease. Thus, considering nutrition facts when deciding what to purchase is important.
Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells1[OPEN]

Two shell protein paralogs of the carboxysome, the carbon dioxide fixation microcompartment in β-cyanobacteria, form heterohexamers that stack into dodecamers, which would alter shell permeability. Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of β-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by “capping” facet-embedded hexamers with a second hexamer. Because β-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.
Distribution of Saponins in the Sea Cucumber Holothuria lessoni; the Body Wall Versus the Viscera, and Their Biological Activities

Sea cucumbers are an important ingredient of traditional folk medicine in many Asian countries, which are well-known for their medicinal, nutraceutical, and food values due to producing an impressive range of distinctive natural bioactive compounds. Triterpene glycosides are the most abundant and prime secondary metabolites reported in this species. They possess numerous biological activities ranging from anti-tumour, wound healing, hypolipidemia, pain relieving, the improvement of nonalcoholic fatty livers, anti-hyperuricemia, the induction of bone marrow hematopoiesis, anti-hypertension, and cosmetics and anti-ageing properties. This study was designed to purify and elucidate the structure of saponin contents of the body wall of sea cucumber Holothuria lessoni and to compare the distribution of saponins of the body wall with that of the viscera. The body wall was extracted with 70% ethanol, and purified by a liquid-liquid partition chromatography, followed by isobutanol extraction. A high-performance centrifugal partition chromatography (HPCPC) was conducted on the saponin-enriched mixture to obtain saponins with a high purity. The resultant purified saponins were analyzed using MALDI-MS/MS and ESI-MS/MS. The integrated and hyphenated MS and HPCPC analyses revealed the presence of 89 saponin congeners, including 35 new and 54 known saponins, in the body wall in which the majority of glycosides are of the holostane type. As a result, and in conjunction with existing literature, the structure of four novel acetylated saponins, namely lessoniosides H, I, J, and K were characterized. The identified triterpene glycosides showed potent antifungal activities against tested fungi, but had no antibacterial effects on the bacterium Staphylococcus aureus. The presence of a wide range of saponins with potential applications is promising for cosmeceutical, medicinal, and pharmaceutical products to improve human health.
A Polygenic Genetic Architecture of Flowering Time in the Worldwide Arabidopsis thaliana Population

Here, we report an empirical study of the polygenic basis underlying the evolution of complex traits. Flowering time variation measured at 10 and 16°C in the 1,001-genomes Arabidopsis thaliana collection of natural accessions were used as a model. The polygenic architecture of flowering time was defined as the 48 loci that were significantly associated with flowering time-at 10 and/or 16°C and/or their difference-in this population. Contributions from alleles at flowering time associated loci to global and local adaptation were explored by evaluating their distribution across genetically and geographically defined subpopulations across the native range of the species. The dynamics in the genetic architecture of flowering time in response to temperature was evaluated by estimating how the effects of these loci on flowering changed with growth temperature. Overall, the genetic basis of flowering time was stable-about 2/3 of the flowering time loci had similar effects at 10°C and 16°C-but many loci were involved in gene by temperature interactions. Globally present alleles, mostly of moderate effect, contributed to the differences in flowering times between the subpopulations via subtle changes in allele frequencies. More extreme local adaptations were, on several occasions, due to regional alleles with relatively large effects, and their linkage disequilibrium-patterns suggest coevolution of functionally connected alleles within local populations. Overall, these findings provide a significant contribution to our understanding about the possible modes of global and local evolution of a complex adaptive trait in A. thaliana.
Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal

ABSTRACT Adult stem cell niche boundaries must be precisely maintained to facilitate the segregation of stem cell and daughter cell fates. However, the mechanisms that govern this process in epithelial tissues are not fully understood. In this study, we investigated the relationship between two signals, Wnt and EGFR, that are necessary for self-renewal of the epithelial follicle stem cells (FSCs) in the Drosophila ovary, but must be downregulated in cells that have exited the niche to allow for differentiation. We found that Wingless produced by inner germarial sheath (IGS) cells acts over a short distance to activate Wnt signaling in FSCs, and that movement across the FSC niche boundary is limited. In addition, we show that Wnt signaling functions genetically upstream of EGFR signaling by activating the expression of the EGFR ligand, Spitz, and that constitutive activation of EGFR partially rescues the self-renewal defect caused by loss of Wnt signaling. Collectively, our findings support a model in which the Wnt and EGFR pathways operate in a signaling hierarchy to promote FSC self-renewal. Summary: This study identifies a hierarchy of niche signaling that maintains Drosophila follicle stem cells and might be important for a robust, yet dynamic, niche.
Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.)

PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.
Analysis of Repeat Induced Point (RIP) Mutations in Leptosphaeria maculans Indicates Variability in the RIP Process Between Fungal Species

Gene duplication contributes to evolutionary potential, yet many duplications in a genome arise from the activity of “selfish” genetic elements such as transposable elements. Fungi have a number of mechanisms by which they limit the expansion of transposons, including Repeat Induced Point mutation (RIP). RIP has been best characterized in the Sordariomycete Neurospora crassa, wherein duplicated DNA regions are recognized after cell fusion, but before nuclear fusion during the sexual cycle, and then mutated. While “signatures” of RIP appear in the genome sequences of many fungi, the species most distant from N. crassa in which the process has been experimentally demonstrated to occur is the Dothideomycete Leptosphaeria maculans. In the current study, we show that similar to N. crassa, nonlinked duplications can trigger RIP; however, the frequency of the generated RIP mutations is extremely low in L maculans (< 0.1%) and requires a large duplication to initiate RIP, and that multiple premeiotic mitoses are involved in the RIP process. However, a single sexual cycle leads to the generation of progeny with unique haplotypes, despite progeny pairs being generated from mitosis. We hypothesize that these different haplotypes may be the result of the deamination process occurring post karyogamy, leading to unique mutations within each of the progeny pairs. These findings indicate that the RIP process, while common to many fungi, differs between fungi and that this impacts on the fate of duplicated DNA.