Miracle-dz/UniFAR-FTUs huggingface dataset:
Rôle du système rénine-angiotensine intrarénal dans l’hypertension et les dommages rénaux chez les souristransgéniques diabétiques

Experimental and clinical studies have shown that renin-angiotensin system (RAS) activation may lead to hypertension, a major cardiovascular and renal risk factor. Angiotensinogen (Agt) is the sole substrate of the RAS. However, it is unclear whether intrarenal RAS activation alone could induce kidney injury independently of systemic hypertension and play an important role in the progression of diabetic nephropathy (DN). To explore the role of intrarenal RAS in kidney injury, transgenic (Tg) mice overexpressing rat Agt in their renal proximal tubular cells (RPTCs) were rendered diabetic by streptozotocin (STZ). Diabetic Tg mice were treated with RAS blockers (perindopril and losartan), insulin or a combination of both and then euthanized after 4 weeks of treatment. In a separate study, non-diabetic Tg mice were treated with RAS blockers or hydralazine (a vasodilator) or apocynin (an NADPH oxidase inhibitor) and then euthanized after 8 weeks of treatment. Non-Tg littermates served as controls in both studies. Immortalized rat proximal tubule cells (IRPTCs) stably transfected with Agt cDNA or control plasmid were used in the experiments as an in vitro model. Our results showed that non-diabetic Tg mice displayed a significant increase in systolic blood pressure (SBP), albuminuria, RPTC apoptosis, and proapoptotic gene expression. Diabetic Tg mice had a further increase of albuminuria, RPTC apoptosis, and proapoptotic gene expression, though the SBP of the diabetic Tg mice was similar to that of non-diabetic Tg mice. RAS blockers and/or insulin treatments markedly attenuated these changes, except that insulin had no impact on hypertension. In vitro, high-glucose melieu significantly increased apoptosis and caspase-3 activity in Agt stable transfectants compared to control cells, and these changes were attenuated by insulin and/or RAS blockers. Furthermore, non-diabetic Tg mice showed significantly elevated reactive oxygen species (ROS) production and NADPH oxidase activity, as well as
Freewater EstimatoR using iNtErpolated iniTialization (FERNET): Toward Accurate Estimation of Free Water in Peritumoral Region Using Single-Shell Diffusion MRI Data

Characterization of healthy versus pathological tissue is a key concern when modeling tissue microstructure in the peritumoral area, confounded by the presence of free water (e.g., edema). Most methods that model tissue microstructure are either based on advanced acquisition schemes not readily available in the clinic, or are not designed to address the challenge of edema. This underscores the need for a robust free water elimination (FWE) method that estimates free water in pathological tissue but can be used with clinically prevalent single-shell diffusion tensor imaging data. FWE in single-shell data requires the fitting of a bi-compartment model, which is an ill-posed problem. Its solution requires optimization, which relies on an initialization step. We propose a novel initialization approach for FWE, FERNET, which improves the estimation of free water in edematous and infiltrated peritumoral regions, using single-shell diffusion MRI data. The method has been extensively investigated on simulated data and healthy and brain tumor datasets, demonstrating its applicability on clinically acquired data. Additionally, it has been applied to data from brain tumor patients to demonstrate the improvement in tractography in the peritumoral region.
Broccoli, cabbage, squash and watermelon response to halosulfuron preplant over plastic mulch

Abstract Nutsedge species are problematic in plastic-mulched vegetable production because of the weed's rapid reproduction and ability to penetrate the mulch. Vegetable growers rely heavily on halosulfuron to manage nutsedge species; however, the herbicide cannot be applied over mulch before vegetable transplanting due to potential crop injury. This can be problematic when multiple crops are produced on a single mulch installation. Field experiments were conducted to determine the response of broccoli, cabbage, squash, and watermelon to halosulfuron applied on top of mulch prior to transplanting. Halosulfuron at 80 g ai ha–1 was applied 21, 14, 7, and 1 d before planting (DBP), and 160 g ai ha–1 was applied 21 DBP. In all experiments, extending the interval between halosulfuron application and planting reduced crop injury. For squash and watermelon, visual injury, plant diameters/vine runner lengths, marketable fruit weights, and postharvest plant biomass resulted in similar values when applying 80 g ha–1 21 DBP and with the nontreated weed-free control. Reducing this interval increased injury for both crops. Visual crop injury and yield reductions up to 40% occurred, with halosulfuron applied 14, 7, or 1 DBP in squash and 1 DBP in watermelon. Broccoli and cabbage showed greater sensitivity, with injury and plant diameter reductions greater than 15%, even with halosulfuron applied at 80 g ha–1 21 DBP. Experimental results confirm that halosulfuron binds to plastic mulch, remains active, and is slowly released from the mulch over a substantial period, during rainfall or overhead irrigation events. Extending the plant-back interval to at least 21 d before transplanting did overcome squash and watermelon injury concerns with halosulfuron at 80 g ha–1, but not broccoli and cabbage. Applying halosulfuron over mulch to control emerged nutsedge before planting squash and watermelon would be beneficial if adequate rainfall or irrigation and appropriate intervals between application and planting are implemented. Nomenclature: Halosulfuron; purple nutsedge, Cyperus rotundus L. ; yellow nutsedge, Cyperus esculentus L. ; broccoli, Brassica oleracea var. botrytis L. ‘Emerald crown'; cabbage, Brassica oleracea var. capitata L. ‘Cheers'; squash, Cucurbita pepo L. ‘Enterprise'; watermelon, Citrullus lanatus (Thunb.) Matsum. & Nakai ‘Sangria'
Improving phosphorus sustainability of sugarcane production in Brazil

Phosphorus (P) use in global food and bioenergy production needs to become more efficient and sustainable to reduce environmental impacts and conserve a finite and critical resource (Carpenter & Bennett, Environmental Research Letters, 2011, 6, 014009; Springmann et al., Nature, 2018, 562, 519). Sugarcane is one crop with a large P footprint because production is centered on P‐fixing soils with low P availability (Roy et al., Nature Plants, 2016, 2, 16043; Withers et al., Scientific Reports, 2018, 8, 2537). As global demand for processed sugar and bioethanol continues to increase, we advocate that improving P efficiency could become a key sustainability goal for the sugarcane industry. Here, we applied the 5R global P stewardship framework (Withers et al., Ambio, 2015, 44, 193) to identify more sustainable options to manage P in Brazilian sugarcane production. We show that current inputs of P fertilizer to the current crop area could be reduced by over 305 Gg, or 63%, over the next three decades by reducing unnecessary P fertilizer use, better utilization of recyclable bioresources and redesigning recommendation systems. Adoption of these 5R options would save the sugarcane industry in Brazil 528 US$ million and help safeguard global food and energy security.
Morphological characterization of Coelogyne spp for germplasm conservation of orchids

Submitted on October 17 , 2018 and accepted on July 29 , 2019. Universitas Sebelas Maret, Faculty of Agriculture, Department of Agrotechnology , Surakarta, Central Java, Indonesia. 2 Universitas Tunas Pembangunan, Faculty of Agriculture, Department of Agrotechnology , Surakarta, Central Java, Indonesia. 3 Center for Plant Conservation-Bogor Botanical Gardens, Indonesian Institute of Sciences, Bogor West Java, Indonesia. *Corresponding author: tatik_oc@yahoo.com Morphological characterization of Coelogyne spp for germplasm conservation of orchids
The complete chloroplast genome of a medical herb, Halenia elliptica D.Don (Gentianaceae), from Qinghai-Tibet Plateau in China

Abstract Halenia elliptica D.Don (Gentianaceae) is one of the genuine medicinal species in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of H. elliptica using Illumina HiSeq X Ten platform. The length of its complete cp genome is 153,341 bp, containing four sub-regions; a large single-copy region (LSC) of 82,811 bp and a small single-copy region (SSC) of 18,278 bp, which are separated by a pair of inverted repeat regions (IRs) of 26,126bp each. The complete cp genome of H. elliptica contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 38.1%. The phylogenetic analysis, based on 15 cp genomes, suggested that H. elliptica is closely related to Halenia corniculata (L.) Cornaz and Swertia species.
Contribution of unfixed transposable element insertions to human regulatory variation

Thousands of unfixed transposable element (TE) insertions segregate in the human population, but little is known about their impact on genome function. Recently, a few studies associated polymorphic TE insertions to mRNA levels of adjacent genes, but the biological significance of these associations, their replicability across cell types, and the mechanisms by which they may regulate genes remain largely unknown. Here we performed a TE-expression QTL analysis of 444 lymphoblastoid cell lines and 294 induced pluripotent stem cells using a newly developed set of genotypes for 2,806 polymorphic TE insertions. We identified 211 and 324 TE-eQTL acting in cis in each respective cell type. Approximately one fourth were shared across cell types with strongly correlated effects. Furthermore, analysis of chromatin accessibility QTL in a subset of the lymphoblastoid cell lines suggests that unfixed TEs often modulate the activity of enhancers and other distal regulatory DNA elements, which tend to lose accessibility when a TE inserts within them. We also document a case of an unfixed TE likely influencing gene expression at the post-transcriptional level. Our study points to broad and diverse cis-regulatory effects of unfixed TEs in the human population and underscores their plausible contribution to phenotypic variation.
A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development

Enhancers that are conserved deep in evolutionary time regulate characteristics held in common across taxonomic classes. Here, deletion of the highly conserved Shh enhancer SBE2 (Shh brain enhancer 2) markedly reduced Shh expression within the embryonic brain specifically in the rostral diencephalon; however, no abnormal anatomical phenotype was observed due to compensatory low levels of expression mediated by a second enhancer. In contrast, a further reduction of Shh levels, achieved by crossing the SBE2 deletion with the Shh null allele, disrupted brain and craniofacial tissue; thus, linking SBE2 regulated Shh expression to multiple defects and further enabling the study of the effects of differing levels of Shh on embryogenesis. Development of the hypothalamus, derived from the rostral diencephalon, was disrupted along both the anterior-posterior (AP) and the dorsal-ventral (DV) axes. Expression of DV patterning genes and subsequent neuronal population induction were particularly sensitive to Shh expression levels, demonstrating a novel morphogenic context for Shh. The role of SBE2, which is highlighted by DV gene expression, is to step-up expression of Shh above the minimal activity of the second enhancer, ensuring the necessary levels of Shh in a regional-specific manner. We also show that low Shh levels in the diencephalon disrupted neighbouring craniofacial development, including mediolateral patterning of the bones along the cranial floor and viscerocranium. Thus, SBE2 contributes to hypothalamic morphogenesis and ensures there is coordination with the formation of the adjacent midline cranial bones that subsequently protects the neural tissue.
Honeydew composition and its effect on life‐history parameters of hyperparasitoids

1. Diets that maximise life span often differ from diets that maximise reproduction. Animals have therefore evolved advanced foraging strategies to acquire optimal nutrition and maximise their fitness. The free‐living adult females of parasitoid wasps (Hymenoptera) need to balance their search for hosts to reproduce and for carbohydrate resources to feed.
Slow degradation of compostable plastic carrier bags in a stream and its riparian area

There is no place on Earth where plastic debris could not be found. Impacts of plastics on aesthetics, biota and ecosystems are dependent on how long plastic items last, and what degradation products are released, in recipient environments. As bio-based plastics tend to replace petroleum-based plastics in everyday life, it is important to upgrade knowledge on the degradation of new polymers in natural environments. Single-use plastic carrier bags are nowadays made of bio-plastics certified as biodegradable and compostable. It is unclear, however, whether claims of biodegradability and compostability can be taken as evidence of rapid degradation of plastic bags outside recycling/composting facilities. This study sought to provide quantified information about the degradation of compostable plastic carrier bags in streams and riparian zones. We found that plastic samples enclosed in different types of mesh bags lost weight at extremely slow rates, albeit significant when submerged in a stream. 95% of initial plastic mass remained after 77 days spent in water whereas alder leaf litter allowed to decompose under the same condition had completely disappeared before the end of the study. Determination of respiration rate and invertebrate abundance in plastic samples showed a greater decomposer activity in the stream than in the riparian environment. However, biotically-mediated degradation by decomposers was probably overridden by dissolution processes in mediating plastic mass loss. Our findings suggest that mismanaged plastic carrier bags could impact recipient ecosystems even when they are claimed as biodegradable or compostable.
Is low-level laser therapy effective in the management of lateral epicondylitis?

The purpose of “Evidence in Practice” is to illustrate how evidence is gathered and used to guide clinical decision making. This article is not a case report. The examination, evaluation, and intervention sections are purposely abbreviated. A 55-year-old woman, who was right-hand dominant, was referred to my physical therapy clinic with a 6-month history of pain in her left lateral elbow. The patient was an assembly-line worker in an automotive factory. She worked 40 to 50 hours per week in a rotating 9-job “loop” manufacturing diesel engines. Each day she would perform a different job in the loop for the duration of her shift, until she had performed all 9 job functions, at which …
A Novel Visual Method for Studying Complex Health Transitions for Older People Living With Dementia

Understanding the complexity of health services for older people living with dementia is a challenging research endeavor. We discuss a novel research approach that combines photographic methods with storyboarding techniques to understand the views of older people living with dementia who encounter the emergency department. A social ecological theoretical position was taken to study relationships between health care systems and processes and the social arrangements of those receiving care. The research approach uncovers complex contextual factors in health care systems that are amenable to change. The approach strengthens the contribution of older people living with dementia to have their voice included in research endeavors.
Dopamine 2 Receptor Signaling Controls the Daily Burst in Phagocytic Activity in the Mouse Retinal Pigment Epithelium

Purpose A burst in phagocytosis of spent photoreceptor outer fragments by retinal pigment epithelium (RPE) is a rhythmic process occurring 1-2 hours after the onset of light. This phenomenon is considered crucial for the health of the photoreceptors and RPE. We have recently reported that dopamine, via dopamine 2 receptor (D2R), shifts the circadian rhythm in the RPE. Methods Here, we first investigated the impact of the removal of D2R on the daily peak of phagocytosis by RPE and then we analyzed the function and morphology of retina and RPE in the absence of D2R. Results D2R KO mice do not show a daily burst of phagocytic activity after the onset of light. Also, in contrast to control, phosphorylation of FAK did not increase significantly in KO mice at ZT1. RNA sequencing revealed a total of 394 differentially expressed genes (DEGs) between ZT23 and ZT1 in the control mice, whereas in D2R KO mice, we detected 1054 DEGs. Pathway analysis of the gene expression data implicated integrin signaling to be one of the upregulated pathways in control but not in D2R KO mice. No difference in retinal thickness, visual function, or morphology of RPE cells was observed between WT and D2R KO mice at the age of 3 and 12 months. Conclusions Our data suggest that removal of D2R prevents the burst in phagocytosis and a related increase in the phosphorylation of FAK after light onset. The pathway analysis points towards a putative role of D2R in controlling integrin signaling, which is known to play an important role in the control of the daily burst of phagocytosis by the RPE. Our data also indicate that the absence in the burst of phagocytic activity in the early morning does not produce any apparent deleterious effect on the retina or RPE up to one year of age.
A tomato kinesin-like protein is associated with Tobacco mosaic virus infection

Abstract Tobacco mosaic virus (TMV) causes severe damage and economic losses of tomato in crop yield production and quality worldwide. Tomato plants infected with TMV usually show a mosaic pattern and chlorosis symptoms that result from affected chloroplasts. To elucidate tomato–TMV interactions, the transcriptional profiles of tomato tissues at different time intervals were analysed using a differential display-polymerase chain reaction technique. Compared to mock-inoculated plants, and based on gene expression changes in tomato plants, the representative down- and up-regulated genes were selected for further analysis. The Basic Local Alignment Search Tool at the National Center for Biotechnology Information (NCBI-BLAST) analysis revealed that the three up-regulated gene transcripts at 15 days post-inoculation were coding for chloroplast (MG565980 and MG565979) and kinesin-like proteins (MG565981). Additionally, the down-regulated gene was a chloroplast-related gene (MG565978). Interestingly, the two chloroplast genes, MG565978 and MG565980, shared more than 96% sequence identity, and their transmembrane profiles were nearly identical. On the other hand, many protein kinase C phosphorylation, casein kinase II phosphorylation and N-myristoylation sites were detected within the MG565981 gene. Moreover, the high similarity between the kinesin gene and many Arabidopsis defensin genes indicated that it might play an important role in the plant defence system against TMV infection. It should be stressed that studies of the pathways in which chloroplast and kinesin-like protein genes are involved may elucidate the mechanisms of tomato tolerance to viral infection and can lead us to a more comprehensive understanding of tomato–TMV interactions.
A strong east–west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

Phylogeography of fruit trees is challenging due to recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the eastern Mediterranean and a feral origin in the west.
A Study on the Relative Performance of Different Coagulants and the Kinetics of COD in the Treatment of a Textile Bleaching and Dyeing Industrial Wastewater

Untreated wastewater from textile industries when discharged to nearby waterways would cause considerable health concerns to humans and animal life and to the host environment. They contain various chemicals such as dyes, detergents and surfactants, some of which are recalcitrant to biodegradation. Such wastewater can be better remediated by chemical treatment. The treatment of a textile bleaching and dyeing industrial wastewater was done by Coagulation and Flocculation Method using a jar test apparatus. Alum, polyaluminum chloride (PAC), and ferrous sulfate were used in separate runs as coagulants, while excelfloc 264 (a polyacrylamide copolymer) was used as flocculant. Preliminary tests were first conducted to determine the appropriate coagulation and flocculation agitation rates and settling time. The initial pH of the sample effluent was varied from 5 to 8 for alum coagulation, 5 to 8.5 for PAC coagulation and 9 to 11 for ferrous sulfate coagulation. The dosages of each coagulant and the excelfloc were varied from 200 to 1000 ppm, and 0.5 to 2.5 ppm, respectively. Experimental results showed that the optimum initial pH of the wastewater using alum, PAC, and ferrous sulfate were 7, 7.5, and 10, respectively. The optimum dosages of the coagulants were found to be 600ppm for alum and 800ppm for both PAC, and ferrous sulfate. The optimum flocculant dosages were 1.5ppm with alum, 1 ppm with PAC and 2ppm with ferrous sulfate. The highest percentage removal of COD, Total Suspended Solids (TSS), Total Dissolved Solids (TDS), chromium, and color were found to be 58.55%, 65%, 36.51%, 76.45%, and 78.96%, respectively, using alum: 65.4%, 67.5%, 35.84%, 44.92%, and 75.49%, respectively using PAC; and, 55.72%, 34.16%, 33.95%, 19.88%, and 48.56%, respectively, using ferrous sulfate. Among the three coagulants tried, coagulation with PAC gave the highest percentage of COD removal of 65.64% and TSS removal of 67.5% while alum gave the highest removal of both chromium and color at 76.45% and 94.49%, respectively. Rapid and slow agitation rates used were 240rpm for 1 minute and 40rpm for 20 minutes, respectively; while settling time was 30 minutes. Kinetics of the COD removal was studied at the optimum conditions. Kinetic model, determined by curve fitting with the coagulation/flocculation reaction, was observed to follow a first-order rate of reaction.