Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Liquid Cattle Manure on Micronutrients Content and Uptake by Corn and their Availability in a Calcareous Soil

The effect of soil application of liquid dairy cattle (Bos taurus) manure on Cu, Zn, Fe, Mn, and B content and uptake by corn (Zea mays L.) and their availability in a calcareous soil was studied. The field received 9 yr of liquid cattle manure in two fertilization experiments, initially with winter wheat (Triticum aestivum L.) (1996-2000), followed by a similar experiment with corn (2002-2006). The treatments, practiced on the same plots every year since 1996, included: (i) soil incorporation ofliquid dairy cattle manure before sowing at a rate equivalent to the recommended N-P inorganic fertilization for each crop; (ii) application of the recommended inorganic N-P fertilization for each crop, before sowing; (iii) identical to ii, but with split N application; and (iv) no fertilization (control). Surface soil samples were analyzed at the beginning of each corn-growing season and in the spring of 2007. Corn samples, collected at the R3 growth stage, were also analyzed. The results showed that concentrations of all micronutrients in corn were not affected by fertilization. However, following manure application in 2005 and 2006, micronutrients' uptake by corn was significantly increased compared to the control, and was similar to levels for the inorganic fertilizer treatments. After 9 yr of manure application to soil, DTPA extractable Cu, Zn, and Mn and hot water extractable B were significantly increased. In addition, soil total and dissolved organic C were significantly increased and dissolved organic C was significantly correlated to DTPA extractable metals.
Emergence of mcr-9.1 in Extended-Spectrum-β-Lactamase-Producing Clinical Enterobacteriaceae in Pretoria, South Africa: Global Evolutionary Phylogenomics, Resistome, and Mobilome

Colistin is currently the last-resort antibiotic for difficult-to-treat bacterial infections. However, colistin resistance genes that can move from bacteria to bacteria have emerged, threatening the safe treatment of many bacterial infections. One of these genes, mcr-9.1, has emerged in South Africa in bacteria that are multidrug resistant, further limiting treatment options for clinicians. In this work, we show that this new gene is disseminating worldwide through Enterobacter and Salmonella species through multiple plasmids. This worrying observation requires urgent action to prevent further escalation of this gene in South Africa and Africa. ABSTRACT Extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae are critical-priority pathogens that cause substantial fatalities. With the emergence of mobile mcr genes mediating resistance to colistin in Enterobacteriaceae, clinicians are now left with few therapeutic options. Eleven clinical Enterobacteriaceae strains with resistance to cephems and/or colistin were genomically analyzed to determine their resistomes, mobilomes, and evolutionary relationships to global strains. The global phylogenomics of mcr genes and mcr-9.1-bearing genomes were further analyzed. Ten isolates were ESBL positive. The isolates were multidrug resistant and phylogenetically related to global clones but distant from local strains. Multiple resistance genes, including blaCTX-M-15 blaTEM-1, and mcr-9.1, were found in single isolates; ISEc9, IS19, and Tn3 transposons bracketed blaCTX-M-15 and blaTEM-1. Common plasmid types included IncF, IncH, and ColRNAI. mcr-9 was of close sequence identity to mcr-3, mcr-5, mcr-7, mcr-8, and mcr-10. Genomes bearing mcr-9.1 clustered into six main phyletic groups (A to F), with those of this study belonging to clade B. Enterobacter species and Salmonella species are the main hosts of mcr-9.1 globally, although diverse promiscuous plasmids disseminate mcr-9.1 across different bacterial species. Emergence of mcr-9.1 in ESBL-producing Enterobacteriaceae in South Africa is worrying, due to the restricted therapeutic options. Intensive One Health molecular surveillance might discover other mcr alleles and inform infection management and antibiotic choices. IMPORTANCE Colistin is currently the last-resort antibiotic for difficult-to-treat bacterial infections. However, colistin resistance genes that can move from bacteria to bacteria have emerged, threatening the safe treatment of many bacterial infections. One of these genes, mcr-9.1, has emerged in South Africa in bacteria that are multidrug resistant, further limiting treatment options for clinicians. In this work, we show that this new gene is disseminating worldwide through Enterobacter and Salmonella species through multiple plasmids. This worrying observation requires urgent action to prevent further escalation of this gene in South Africa and Africa.
Theiler's murine encephalomyelitis virus and mechanisms of its persistence

Theiler's murine encephalomyelitis virus (TMEV) is divided into two subgroups: GDVII and DA (or TO). The GDVII subgroup strains are highly virulent and produce acute polioencephalomyelitis in mice. Neither viral persistence nor demyelination occurs. In contrast, the DA (or TO) subgroup strains are less virulent and establish a persistent infection in the spinal cords of mice, despite a vigorous humoral immune response, followed by chronic demyelination. Theiler's murine encephalomyelitis virus is an excellent animal model for the human demyelinating disease multiple sclerosis. Several interesting features regarding TMEV persistence have been reported. A majority of TMEV‐infected cells during the chronic stage of the disease contain only 100–500 copies of the genome, which is less than the number necessary for detectable expression of viral proteins. The limited viral protein synthesis probably induces relatively little cytopathic effect and also allows the virus to bypass immunological clearance. Sequence analysis of escape mutant viruses resistant to DA neutralizing monoclonal antibodies identified four separate amino acid mutations of capsid proteins, all of which are located on or near the rim of the ‘pit’, a putative receptor binding region of the virus. In addition, mutant viruses demonstrated a decrease of demyelinating activity. These findings suggest that antibody mediates neutralization by preventing the binding of virus to the cell receptor and that demyelination with virus persistence can be interfered with by preventing viral attachment to receptors of particular cell types. Finally, a 17 kDa protein, designated as L*, is synthesized in DA subgroup strains from an alternative, out‐of‐frame initiation site. Studies of a DA mutant virus without L* protein synthesis demonstrated that this protein is important for virus growth in particular cell types and is critical for DA‐induced demyelinating disease and virus persistence.
Multi-Level Cross Residual Network for Lung Nodule Classification

Computer-aided algorithm plays an important role in disease diagnosis through medical images. As one of the major cancers, lung cancer is commonly detected by computer tomography. To increase the survival rate of lung cancer patients, an early-stage diagnosis is necessary. In this paper, we propose a new structure, multi-level cross residual convolutional neural network (ML-xResNet), to classify the different types of lung nodule malignancies. ML-xResNet is constructed by three-level parallel ResNets with different convolution kernel sizes to extract multi-scale features of the inputs. Moreover, the residuals are connected not only with the current level but also with other levels in a crossover manner. To illustrate the performance of ML-xResNet, we apply the model to process ternary classification (benign, indeterminate, and malignant lung nodules) and binary classification (benign and malignant lung nodules) of lung nodules, respectively. Based on the experiment results, the proposed ML-xResNet achieves the best results of 85.88% accuracy for ternary classification and 92.19% accuracy for binary classification, without any additional handcrafted preprocessing algorithm.
Vitamin D and Cardiovascular Risk: Which Implications in Children?

Vitamin D (25OHD) pleiotropic effects are widely recognized and studied. Recently, vitamin D cardiovascular effects are gaining interest, especially in children, although the studies present conflicting data. Some randomized controlled trials (RCTs) have demonstrated that cardiovascular risk markers, such as lipid parameters, inflammation markers, blood pressure, and arterial stiffness, are unaffected by vitamin D supplementation. By contrast, other studies show that low vitamin D levels are associated with higher risk of cardiovascular disease (CVD) and mortality, and support that increased risk of these diseases occurs primarily in people with vitamin D deficiency. An update on these points in pediatric patients is certainly of interest to focus on possible benefits of its supplementation.
Effect of violet LED light on in-office bleaching protocols: a randomized controlled clinical trial

Abstract Objective This study evaluated the clinical effect of violet LED light on in-office bleaching used alone or combined with 37% carbamide peroxide (CP) or 35% hydrogen peroxide (HP). Methodology A total of 100 patients were divided into five groups (n=20): LED, LED/CP, CP, LED/HP and HP. Colorimetric evaluation was performed using a spectrophotometer (ΔE, ΔL, Δa, Δb) and a visual shade guide (ΔSGU). Calcium (Ca)/phosphorous (P) ratio was quantified in the enamel microbiopsies. Measurements were performed at baseline (T 0 ), after bleaching (T B ) and in the 14-day follow-up (T 14 ). At each bleaching session, a visual scale determined the absolute risk (AR) and intensity of tooth sensitivity (TS). Data were evaluated by one-way (ΔE, Δa, ΔL, Δb), two-way repeated measures ANOVA (Ca/P ratio), and Tukey post-hoc tests. ΔSGU and TS were evaluated by Kruskal-Wallis and Mann-Whitney, and AR by Chi-Squared tests (a=5%). Results LED produced the lowest ΔE (p<0.05), but LED/HP promoted greater ΔE, ΔSGU and Δb (T 14 ) than HP (p<0.05). No differences were observed in ΔE and ΔSGU for LED/CP and HP groups (p>0.05). ΔL and Δa were not influenced by LED activation. After bleaching, LED/CP exhibited greater Δb than CP (p>0.05), but no differences were found between these groups at T 14 (p>0.05). LED treatment promoted the lowest risk of TS (16%), while HP promoted the highest (94.4%) (p<0.05). No statistical differences of risk of TS were found for CP (44%), LED/CP (61%) and LED/HP (88%) groups (p>0.05). No differences were found in enamel Ca/P ratio among treatments, regardless of evaluation times. Conclusions Violet LED alone produced the lowest bleaching effect, but enhanced HP bleaching results. Patients treated with LED/CP reached the same efficacy of HP, with reduced risk and intensity of tooth sensitivity and none of the bleaching protocols adversely affected enamel mineral content.
Work, living, and the pursuit of happiness: Vocational and psychosocial outcomes for young adults with autism

Longitudinal data on the functioning of adults referred for possible autism as children are sparse and possibly different from datasets consisting of adult clinical referrals. A total of 123 young adults, mean age of 26, referred for neurodevelopmental disorders in early childhood were categorized into three outcome groups: autism spectrum disorder (ASD) diagnosis at some point and current intelligence quotient (IQ) ⩾ 70 (Ever ASD-Higher IQ), ever ASD and current IQ < 70 (Ever ASD-Lower IQ), and individuals who never received an ASD diagnosis (Never ASD). Independence and well-being were assessed through direct testing, questionnaires, and interviews. Verbal IQ, beyond intellectual disability status, accounted for group differences in employment; autistic features (Autism Diagnostic Observation Schedule Calibrated Severity Score) were uniquely related to adaptive skills and friendships. In many ways, the Never ASD group had similar outcomes compared to the ASD groups. However, lower well-being and fewer positive emotions were related to ASD diagnosis across IQ. The Ever ASD-Lower IQ group had the highest levels of irritability, hyperactivity, and medications. Families played a major role in supporting adults with and without ASD at all intellectual levels. Realistic ways of increasing independence should be developed through working with adults and their families, while acknowledging the contribution of individual differences in mental health, intelligence, and autism symptoms across neurodevelopmental disorders. Lay abstract It is important to better understand how adults with autism are functioning in adulthood. Studies that have tracked individuals across the lifespan can help identify developmental factors influence differences in adult outcomes. The present study examines the independence, well-being, and functioning of 123 adults that have been closely followed since early childhood. Autism diagnosis and cognitive assessments were given frequently throughout childhood and during adulthood. We examined differences between adults who had received an autism diagnosis at some point with higher cognitive abilities (Ever ASD-High IQ) and lower cognitive abilities (Ever ASD-Low IQ), as well as adults who never received a diagnosis of autism in the course of the study (Never ASD). We found that autistic features specifically related to adaptive skills and friendships, and verbal intelligence related to work outcomes. In many ways, the Never ASD group had similar outcomes compared to the ASD groups. However, adults with ASD tended to have lower well-being and fewer positive emotions. Families played a major role in supporting adults with and without ASD at all intellectual levels. The findings suggest that realistic ways of increasing independence need to be developed by working with adults and their families, while acknowledging the contribution of individual differences in mental health, intelligence and autism symptoms across neurodevelopmental disorders.
The effect of crude oil on the morphology of the green flagellate Chlamydomonas angulosa

The morphological changes of Chlamydomonas angulosa induced by treatment with an aqueous crude oil extract (ACOE) have been studied and compared with normal cells in the exponential phase of growth. Observations of oil-treated cells under the light microscope showed an effect on flagellar length and on motility, an increased activity of the contractile vacuoles, and an increase in granulations. Cells so treated become surrounded by a transparent envelope. By electron microscopy, the progression of ultrastructural changes has been followed. These changes include: a widened space between the cell wall and the plasmalemma; distorted and disorganized chloroplast lamellae; a decrease in density of the osmiophilic granules; and the presence of electron-dense deposits inside the cytoplasmic vacuoles. Cells were found to possess the ability to recover from the above abnormalities within an 8-day incubation period. Such a recovery corresponds to resumption of motility, capacity for growth, and photosynthesis, as d.
Effect of perches and solid sides on production, plumage and foot condition of laying hens housed in conventional cages in a naturally ventilated shed

The effect of modified cages on production, shell quality, feather cover and foot condition was measured in 2 Australian commercial laying strains housed in a naturally ventilated laying shed from 18 to82 weeks of age. Two cage modifications were investigated. Firstly , the inclusion of a perch within the cage, and secondly, the installation of solid sides. Compared with normal cages, installation of a perch in a cage reduced food intake (5.3%) and liveweight (4.5% at 82 weeks) and improved feather cover around the vent (feather score of 2.15 to 2.66). This was offset by a decrease in egg production (2.4%), shell weight (1.5%) and thickness (11%), an increase in cracked (53.8%) and dirty eggs (28.9%), and an increase in claw length (9.2%). Relative to control cages, the provision of solid sides in cages improved overall feather cover of hens (feather score of 2.46 to 2.67), but there was a 54.5% increase in hen mortality during a period of hot weather. Additional modifications to the cage are required to optimise the benefit of perches. Similarly, improvement in ventilation and cooling in naturally ventilated sheds are required to maximise the benefits of solid-sided cages for hens and avoid heat stress.
Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in Aspergillus nidulans

The transcriptome and phosphoproteome of the filamentous fungus Aspergillus nidulans was monitored after cell wall stress. Over 1800 genes and 700 phosphorylation sites showed dynamic expression and occupancy, respectively. These data guided selection of kinase deletion strains for testing for cell-wall related phenotypes. Kinase-substrate analysis revealed possible connections between CWIS, SIN, HOG, and calcium pathways. Fungi exposed to wall stress experience an increase in septation formation, which may function as a biological defense mechanism. Graphical Abstract Highlights Dynamic transcriptomic and phosphoproteomic study of response to cell-wall stress. MARS model identifies significantly dynamic gene expression and phosphorylation. Septation formation increases during cell-wall stress (via micafungin exposure). Cell wall phenotype assays identified 8 putative CWIS related kinases. The fungal cell-wall integrity signaling (CWIS) pathway regulates cellular response to environmental stress to enable wall repair and resumption of normal growth. This complex, interconnected, pathway has been only partially characterized in filamentous fungi. To better understand the dynamic cellular response to wall perturbation, a β-glucan synthase inhibitor (micafungin) was added to a growing A. nidulans shake-flask culture. From this flask, transcriptomic and phosphoproteomic data were acquired over 10 and 120 min, respectively. To differentiate statistically-significant dynamic behavior from noise, a multivariate adaptive regression splines (MARS) model was applied to both data sets. Over 1800 genes were dynamically expressed and over 700 phosphorylation sites had changing phosphorylation levels upon micafungin exposure. Twelve kinases had altered phosphorylation and phenotypic profiling of all non-essential kinase deletion mutants revealed putative connections between PrkA, Hk-8–4, and Stk19 and the CWIS pathway. Our collective data implicate actin regulation, endocytosis, and septum formation as critical cellular processes responding to activation of the CWIS pathway, and connections between CWIS and calcium, HOG, and SIN signaling pathways.
Indexation of left ventricular mass to predict adverse clinical outcomes in pre-dialysis patients with chronic kidney disease: KoreaN cohort study of the outcome in patients with chronic kidney disease

Background No study has compared the clinical impact of indexation of left ventricular mass (LVM) on adverse clinical outcomes in pre-dialysis patients with chronic kidney disease (CKD). Methods We reviewed 2,101 patients from a large-scale multi-center prospective study that gathered anthropometric and echocardiographic measurements and clinical outcomes. The LVM was indexed as body surface area (LVMI-BSA) and height raised to the power of 2.7 (LVMI-H2.7). The main outcomes were composite renal and cardiovascular events and all-cause mortality. Left ventricular hypertrophy (LVH) was defined as the highest sex-specific quartile of LVMI-BSA or LVMI-H2.7. Results During a mean period of 3.5 years, 692 patients developed composite outcomes (32.9%). The area under the curve at 5 year of LVM (60.6%) for composite outcome was smaller than that for LVMI-BSA (63.2%, P <0.001) and LVMI-H2.7 (63.4%, P <0.001). The hazard ratio (HR) and 95% confidence interval (CI) per one unit increase in LVM (g), LVMI-BSA (g/m2), and LVMI-H2.7 (g/m2.7) for composite outcomes were 1.004 (1.002–1.005, P <0.001), 1.011 (1.006–1.016, P <0.001), and 1.023 (1.012–1.035, P <0.001), respectively. Patients with LVH determined by LVMI-BSA and LVMI-H2.7 (HR 1.352, 95% CI 1.123–1.626, P = 0.001) and LVH determined by only LVMI-BSA (HR 1.908, 95% CI 1.233–2.953, P = 0.004) showed an independent increase in the risk of composite-outcome development, when compared with patients without LVH, according to LVMI-BSA and LVMI-H2.7. Conclusion Indexation of LVM improved the prediction of adverse outcomes. BSA may be as useful as height2.7 in indexing of LVM for predicting adverse outcomes in pre-dialysis patients with CKD.
Trop2 is upregulated in the transition to dysplasia in the metaplastic gastric mucosa

Intestinal‐type gastric adenocarcinoma arises in a field of pre‐existing metaplasia. While biomarkers of cancer and metaplasia have been identified, the definition of dysplastic transition as a critical point in the evolution of cancer has remained obscure. We have evaluated Trop2 as a putative marker of the transition from metaplasia to dysplasia in the stomach in multiple mouse models of metaplasia induction and progression. In addition, TROP2 expression was evaluated in human samples by immunostaining tissue microarrays for metaplasia, dysplasia, and gastric cancer. Dysplastic mouse organoids were evaluated in vitro following shRNA knockdown of Trop2 expression. In mouse models, no Trop2 was observed in the normal corpus and Trop2 was not induced in acute models of metaplasia induction with either L635 or DMP‐777. In Mist1‐Kras mice, Trop2 expression was not observed in metaplasia at 1 month after Kras induction, but was observed in dysplastic glands at 3–4 months after Kras induction. In human tissues, no Trop2 was observed in normal corpus mucosa or SPEM, but Trop2 expression was observed in incomplete intestinal metaplasia, with significantly less expression in complete intestinal metaplasia. Trop2 expression was observed in all dysplastic and 84% of gastric cancer lesions, although expression levels were variable. Dysplastic mouse organoids from Mist1‐Kras mice expressed Trop2 strongly. Knockdown of Trop2 with shRNA markedly reduced organoid growth and budding behavior, and induced the upregulation of apical villin expression. We conclude that Trop2 is upregulated in the transition to dysplasia in the stomach and promotes dysplastic cell behaviors. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.