Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitric oxide enhances the adaptive responses of lupine plants against heavy-metal stress

The present work investigates the possible protective role of nitric oxide (NO) against heavy metals stress in Lupinus termis L. plants. A greenhouse experiment was conducted as a 2 x 2 factorial design with five replications. Lupine seedlings were treated with two concentrations (0.4 mM and 0.6 mM) of sodium nitroprusside (SNP as an NO donor) and subjected to high levels of nickel (Ni) sulfate (100 and 150 mM). The toxic effects of Ni on L. termis plants were evaluated by measuring the oxidative stress markers such as lipid peroxidation, hydrogen peroxide and electrolyte leakage. In addition, growth parameters, endogenous phytohormones, photosynthetic pigment, calcium, magnesium and Ni accumulation in lupin plants grown under Ni toxicity in the presence or absence of NO were also determined. Carbohydrate, organic acid and proline contents were also measured to determine the possible NO-mediated defense strategies in lupine plants to resist Ni stress. The obtained results proved that, Ni toxicity resulted in significantly elevated levels of oxidative stress markers, as well as abscisic acid, jasmonic acid and proline contents, which are associated with significant reduction in growth parameters, photosynthetic pigments, carbohydrate, indole acetic acid and gibberellic acid contents compared with control plants. SNP treatments significantly alleviated the toxic effect of Ni on Lupinus termis L. and increased the amounts of proline, soluble sugars and polysaccharides in shoots and roots, which could be an induced defensive mechanism against heavy-metal stress. Treatment with 0.4 mM SNP was more effective in increasing lupine plants tolerance to Ni toxicity than the 0.6 mM SNP.
In vitro effects of human umbilical cord mesenchymal stem cells on airway secretions of ventilator associated pneumonia in newborns

Objective To explore the effect and its possible mechanism of human umbilical cord mesenchymal stem cells (hUCMSCs) on bacterial growth in bronchoalveolar lavage fluid (BALF) of newborns with ventilator associated pneumonia (VAP). Methods Newborns admitted to neonatal intensive care unit (NICU) in Guangdong Women and Children Hospital Affiliated to Guangzhou Medical University from June 1,2012 to December 31,2012 were reviewed.The inclusion criteria were:(1)Positive BALF culture results. (2) Requirement of mechanical ventilation with tracheal intubation. (3) Diagnosed as ventilator-associated pneumonia.Two pieces of BALF samples of newborn were collected and randornaly divided into experimental and control group.hUCMSCs were added into the experimental group,while the same volume of conditioned medium was added into the control group.Both groups were incubated for six hours in humidified CO2 incubator at 37 ℃,then,bacterial growth was assessed by colony forming unit (CFU) counts.Levels of the antimicrobial peptides (Cathelicidin/LL-37 and human HBD-2) were determined by enzyme-linked immunosorbent assay and Western blot.Paired t-test was used for statistical analysis.Results Among the culture results of 31 newborns,there were Klebsiella pneumoniae (6 cases,19.3％),Stenotrophomonas narrow food aeromonas (6 cases,19.3％),Hemolytic staphylococci (5 cases,16.1％),Escherichia coli (3 cases,9.7％),Bacterial meningitis septicemia Elizabeth Platinum (3 cases,9.7％),Acinetobacter baumannii (3 cases,9.7％),Pseudomonas putida (2 cases,6.4％),Pseudomonas aeruginosa (1 case,3.2％),Staphylococcus aureus (1 case,3.2％) and Enterobacter cloacae (1 ease,3.2％). The CFU counts in experimental group were much less than those in control group [(2.60±0.67) ×104] CFU/ml vs [(1.18±0.32) ×105] CFU/ml,(t=-20.19,P＜0.01). Levels of Cathelicidin/LL-37 and HBD-2 in experimental group were higher than those in control group [Cathelicidin/LL-37:(8.98 ± 3.22) ng/ml vs (3.18 ± 1.57) ng/ml,t =17.79,P ＜ 0.01 ;HBD-2:(379.87±11.74) pg/ml vs (39.89±2.86) pg/ml,t=37.62,P＜0.01]. Conclusions hUCMSCs had antimicrobial effect on bacterial growth in BALFs from ventilator associated pneumonia possibly by the secretion of antimicrobial peptides (Cathelicidin/LL-37 and HBD-2). Key words: Umbilical cord; Mesenchymal stem cells; Pneumonia; Ventilators, mechanical; Catheter-related infections; Bronchoalveolar levage fluid; Cathelicidins; beta-Defensins
Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment

Microsatellite sequences are widely assumed to evolve neutrally, but also play an important role in bacterial pathogenesis, human disease and transcript abundance. The malaria parasite Plasmodium falciparum genome is extraordinarily AT-rich, containing 132,449 microsatellites-stretches of perfect 1-9 bp repeats between 10-1000bp, which comprise 10.74% of the 23 Mb genome. This project was designed to determine the mode and tempo of microsatellite mutations in malaria parasites. We maintained 31 parasite lines derived from a single 3D7 parasite cell for 114-267 days, with frequent bottlenecking to a single cell to minimize effective population size, allowing us to measure mutations accumulated over ~13,207 mitotic divisions. We Illumina sequenced the genomes of both progenitor and end-point mutation accumulation (MA) parasite lines in duplicate to validate stringent calling parameters. Calls were 99.89% (GATK), 99.99% (freeBayes) and 99.96% (HipSTR) concordant in duplicate sequence runs from independent sequence libraries. We observed 98 microsatellite mutations, giving rates of 2.11 × 10-7 - 1.46 × 10-8 /cell division that were strongly influenced by repeat motif and array length. Mutation rate was low relative to other organisms. However, despite this, in a single infection (1011 parasites) there will be 1.46 × 103 - 2.11 × 104 independent mutations at any single microsatellite locus. Given that many microsatellites are found in promotors, introns, within or close to coding sequences, we suggest that they may be important regulators of transcriptional and phenotypic variation in this pathogen. Author summary Mutation is central to evolution: in pathogens, the rate of mutation may determine how rapidly drug resistance evolves or how effectively pathogens can escape immune attack. Malaria parasites have small extremely AT-rich genomes, and genetic variation in natural populations is dominated by repeat number changes in short tandem repeats (microsatellites) rather than point mutations. We therefore focused on quantifying microsatellite mutation. We established 31 parasite cultures in the laboratory all derived from a single parasite cell. These were maintained for 114-267 days with frequent reductions to a single cell, so parasites accumulated mutations during ~13,207 cell divisions. We sequenced the parasite genomes at the end of the experiment to count the mutations. We highlight several conclusions: like other organisms studied, microsatellite mutation rates are associated with both repeat number and repeat motif. However, 41% of changes resulted from loss or gain of more than one repeat: this was particularly true for long repeat arrays. Unlike other eukaryotes, we found no insertions or deletions that were not associated with repeats or homology regions. Overall, we found that microsatellite mutation rates in malaria were amongst the lowest recorded and comparable to those in another AT-rich protozoan (the slime mold Dictyostelium).
E2M: A Deep Learning Framework for Associating Combinatorial Methylation Patterns with Gene Expression

Motivation We focus on the new problem of determining which methylation patterns in gene promoters strongly associate with gene expression in cancer cells of different types. Although a number of results regarding the influence of methylation on expression data have been reported in the literature, our approach is unique in so far that it retrospectively predicts the combinations of methylated sites in promoter regions of genes that are reflected in the expression data. Reversing the traditional prediction order in many cases makes estimation of the model parameters easier, as real-valued data are used to predict categorical data, rather than vice-versa; in addition, our approach allows one to better assess the overall influence of methylation in modulating expression via state-of-the-art learning methods. For this purpose, we developed a novel neural network learning framework termed E2M (Expression-to-Methylation) to predict the status of different methylation sites in promoter regions of several bio-marker genes based on a sufficient statistics of the whole gene expression captured through Landmark genes. We ran our experiments on unquantized and quantized expression sets and neural network weights to illustrate the robustness of the method and reduce the storage footprint of the processing pipeline. Results We implemented a number of machine learning algorithms to address the new problem of methylation pattern inference, including multiclass regression, canonical correlation analysis (CCA), naive fully connected neural network and inception neural networks. Inception neural networks such as E2M learners outperform all other techniques and offer an average prediction accuracy of 82% when tested on 3,671 pan-cancer samples including low grade glioma, glioblastoma, lung adenocarcinoma, lung squamus cell carcinoma, and stomach adenocarcinoma. As an illustrative example, one can increase the prediction accuracy for the methylation pattern in the promoter of gene GATA6 in glioblastoma samples by 20% when using inception rather than simple fully connected neural networks. These performance guarantees remain largely unchanged even when both expression values and network weights are quantized. Our work also provides new insight about the importance of specific methylation site patterns on expression variations for different genes. In this context, we identified genes for which the overwhelming majority of patients exhibit one methylation pattern, and other genes with three or more significant classes of methylation patterns. Inception networks identify such patterns with high accuracy and suggest possible stratification of cancers based on methylation pattern profiles. Availability The E2M code and datasets are freely available at https://github.com/jianhao2016/E2M Contact idoia@illinois.edu, milenkov@illinois.edu
Gestão de Mudança no Projeto De um Novo Produto: O Caso do Fundo Garantidor para Investimentos

This article analyzes from the change management perspective, the implementation of a guarantee fund managed by the BNDES, the Investment Guarantee Fund (FGI), which provides additional guarantees for very small, small and medium enterprises (VSMEs). For this analysis, we used change and stakeholder management models in projects, innovation in financial services and products, and guarantee schemes. The methodology used was a single case study conducted with the fund manager, with documental analysis and semi-structured interviews. The results of the analysis indicate that the corrections in the direction and pace in the Fund’s project implementation, together with stakeholder management techniques application and change management/control in project scope, led to greater security in the Fund’s implementation. This context prevents various risks associated with the operation and adequacy of the final product, contributing to a gradual but steady adoption of the Fund's guarantee by financial agents.
Spontaneous Ischemic Events in the Brain and Heart Adapt the Hearts of Severely Atherosclerotic Mice to Ischemia

To investigate if spontaneous ischemic events in mice with severe multi-organ atherosclerosis could adapt to ischemia, apolipoprotein E/LDL receptor knockout mice were fed an atherogenic diet for 7 to 9 months. Signs of spontaneous ischemia occurred. One to two days later, hearts were excised, Langendorff-perfused with induced global ischemia, and compared with mice without signs of disease. In vivo heart or brain infarctions were verified by heart histology and/or increased serum levels of cardiac troponin T and S100B. Hearts of mice with spontaneous ischemic events had improved function and reduced Langendorff-induced infarctions. To investigate the remote preconditioning effect of brain ischemia, bilateral ligation of the internal carotid arteries was performed in C57BL6 mice. Twenty-four hours later, their isolated hearts were protected against induced global ischemia. A possible role of inducible NO synthase (iNOS) was studied in iNOS knock out mice, who were not preconditioned by induced brain ische.
Island biogeography theory explains the genetic diversity of a fragmented rock ptarmigan (Lagopus muta) population

Abstract The island biogeography theory is one of the major theories in ecology, and its applicability to natural systems is well documented. The core model of the theory, the equilibrium model of island biogeography, predicts that species diversity on an island is positively related to the size of the island, but negatively related by the island's distance to the mainland. In recent years, ecologists have begun to apply this model when investigating genetic diversity, arguing that genetic and species diversity might be influenced by similar ecological processes. However, most studies have focused on oceanic islands, but knowledge on how the theory applies to islands located on the mainland (e.g., mountain islands, forest islands) is scarce. In this study, we examined how the size and degree of isolation of mountain islands would affect the genetic diversity of an alpine bird, the rock ptarmigan (Lagopus muta). Within our study area, we defined the largest contiguous mountain area as the mainland, while smaller mountains surrounding the mainland were defined as islands. We found that the observed heterozygosity (H o) was significantly higher, and the inbreeding coefficient (F is) significantly lower, on the mainland compared to islands. There was a positive significant relationship between the unbiased expected heterozygosity (H n.b.) and island size (log km2), but a negative significant relationship between H o and the cost distance to the mainland. Our results are consistent with the equilibrium model of island biogeography and show that the model is well suited for investigating genetic diversity among islands, but also on islands located on the mainland.
A new type of phlogopite crystal in machineable glass ceramics

Une nouvelle variete de fluorophlogopite a ete mise en evidence dans une vitroceramique du systeme SiO 2 -Al 2 O 3 -MgO-Na 2 O/K 2 O-F − . L'aptitude a l'usinage de cette nouvelle variete est 4 a 5 fois superieure a celle de vitroceramique a base de phlogopite en «chateau de cartes». La nucleation et la cristallisation de cette phase durant le traitement thermique est due a une separation de phase au sein du verre d'origine
In the chick embryo, estrogen can induce chromosomally male ZZ left gonad epithelial cells to form an ovarian cortex which supports oogenesis

In chicken, as in most amniotes, the first morphogenetic event in ovary differentiation is the formation of two distinct domains: a steroidogenic core, the medulla, overlain by the germ cell niche, the cortex. This process normally starts immediately after sex determination in the ZW embryos, substantially before the progression of germ cells into meiosis. In order to address the extent to which the cortical domain depends on intrinsic or extrinsic factors, we generated models of gonadal intersex by mixing ZW (female) and ZZ (male) cells in gonad chimera, or by altering estrogen levels of ZZ and ZW embryos in ovo. We found that both female and male cells can become part of the cortical domain and that this can form relatively independently of the sex of the medulla as long as estrogen is provided. We also show that the cortex promoting activity of estrogen signalling is mediated via Estrogen Receptor alpha within the left gonad epithelium. Either a ZW or ZZ cortical domain thus provides an adequate niche which allows the germ cells to progress into meiosis. However, the presence of a medulla with an “intersex” or male phenotype may compromise this progression, causing cortical germ cells to remain in an immature state in the embryo. This makes meiotic entry a checkpoint for a coordinated sexual differentiation along the female pathway of cortex and medulla.
Feeding and postruminal infusion of calcium gluconate to lactating dairy cows

Abstract: Gluconic acid was proposed as a prebiotic for nonruminants; however, a ruminant application is undescribed. The first experiment was a 5 × 5 Latin square with five test doses of calcium gluconate (CaG) at 0, 5, 17, 32, and 46 g d-1. Treatments were infused into the abomasum of lactating dairy cows for 28 d and milk was collected on days 26, 27, and 28. The second experiment was a crossover where cows (N = 30) were fed a total mixed ration (TMR) with (0.2% of dry matter) and without CaG for 28 d. Milk (days 26, 27, and 28) and blood (day 28) were collected from all cows and rumen fluid (day 28) from a subset of six rumen-cannulated cows. Infusion of CaG into the abomasum increased milk fat yield and decreased dry matter intake resulting in improved feed efficiency. In contrast, cows fed CaG in the TMR had decreased milk yield and milk protein and lactose yields compared with control. In the subset of rumen-cannulated cows, the proportion of butyric acid was decreased and acetic acid increased relative to total volatile fatty acid in cows fed CaG. These findings suggest that CaG utilization may be different in the rumen and lower gastrointestinal tract.
On a Class ofWeakly Berwald (α, β)- metrics of Scalar flag curvature

In this paper, we study two important class of (α, β)-metrics F = α+kβ 2 /α (where k≠0 a constant) and F = α + β + β 2 /α + β 3 /α 2 are of scalar flag curvature. We proved that these metrics are weak Berwald if and only if they are Berwald and their flag curvature vanishes. Further, we found these metrics are locally Minkowskian.
Phytohemagglutinin content in fresh kidney bean in China

ABSTRACT Fresh kidney beans (Phaseolus vulgaris L.) are common green vegetable that are widely cultured and consumed worldwide. The benefits of fresh kidney beans are highly substantial, but at the same time, toxicity caused by phytohemagglutinin (PHA) has raised concerns. PHA from fresh kidney beans accounted for 40% of poisoning events induced by poisonous plants in China from 2004 to 2013. However, an understanding of PHA levels in fresh kidney beans remains elusive. An analysis method for PHA based on agglutination of PHA to erythrocyte cell was established. We investigated the effect of cultivar, bean part, maturity, and cooking method on PHA content in fresh kidney beans. We demonstrated significant differences in the distribution of PHA among various predominant, fresh Chinese kidney bean cultivars and parts. One major Chinese strain, Zihuayoudou, was found to contain the highest amount of PHA, which was abundant in fresh kidney bean seeds. Moreover, PHA concentrations were found to decrease with the maturity of the fresh product. Further, cooking methods had a significant effect on PHA levels in fresh kidney beans. PHA could be effectively removed when stir-frying for more than 18 min, or braising for more than 10 min. These findings provide insight into the PHA content of fresh kidney beans in China and will be helpful to guide food safety measures.
Effect of protein and carbohydrate feed concentrations on the growth and composition of black soldier fly (Hermetia illucens) larvae

Black soldier flies (Hermetia illucens) can be used for a wide range of applications, from screening their anti-microbial properties, entomophagy through to waste management. Although the use of black soldier flies for these purposes has been widely studied, mass-rearing black soldier flies is still in the preliminary phase. This study focussed on the nutritional composition of black soldier fly larvae over the course of their life history, and the impact of manipulating dietary protein and carbohydrate on the growth and composition (protein and fat) of the larvae. Larvae were collected every 24 h over the course of this life-stage to test for differences in composition. To test the effect of dietary protein and carbohydrate differences, larvae were fed 25 diets with varying concentrations of protein and carbohydrates. Overall, the composition of larvae changed very little over their life history, with the higher concentration of protein mostly observed in the earlier instars of the larvae. The pre-pupal stage reduced the fresh and dry weight of the larvae, whereas the ash concentration was very stable throughout their life history. Both dietary protein and dietary carbohydrate had a significant effect on the fresh and dry weight of the larvae, but dietary protein was a stronger indicator of larval fresh and dry weight than dietary carbohydrate. Larval composition was also influenced by the feed-type, with heavier larvae producing significantly more fat than the lighter ones.
Opposition Method based test bench for characterization of SiC Dual MOSFET Modules

Silicon Carbide (SiC) technology is pushing the limits of switching devices in three directions: higher blocking voltage, higher operating temperature and higher switching speed. Nowa-days, samples of Silicon Carbide (SiC) MOSFET modules are available on the market. To evaluate the interest of these new devices in railway applications a first set of measurements, based on a single pulse test bench, was achieved. To complete this work, the authors pro-pose to use the opposition method to compare Si IGBT and SiC MOSFET modules in a volt-age source inverter (VSI) operation. For this purpose, a test bench, allowing electrical and thermal measurements, was developed. Experimental results confirm the theoretical losses calculation coming from the single pulse tests.
Distribution of Eunotia parasiolii (Bacillariophyceae) in Neotropical rivers (Colombia) and its implication on the species's taxonomy

Background. Microorganisms have traditionally been considered cosmopolitan. Nevertheless, recent studies of diverse groups demonstrated that this is an erroneous concept. Reviews of diatoms from the Neotropics have shown high biodiversity and numerous endemic species. Colombia has great habitat diversity in relatively small areas due to its latitudinal position and topography, so it is an ideal site for biogeographic studies. One of the better represented genera in lowland rivers, Eunotia and Eunotia parasiolii, a Neotropical species, was reported in several countries in the region. Goals. In order to establish whether the three morphotypes found are discrete taxonomic entities, their morphometric data, fine morphology and geographical distribution were analyzed. Methods. 170 periphyton samples corresponding to 83 lotic systems were analyzed. Samples were prepared following the CENT/TC 230 (2002) protocol. They were observed with light (LM) and scanning electronic microscope (SEM). Distribution maps were made using GIS and a Moran’s I autocorrelation spatial index was applied. Results. The analyses of several specimens collected at 83 lotic systems allowed us to differentiate a priori 3 morphotypes based on the valve outline, development of subapical costae, and striae density. The species was extensively distributed in the study area, in basins with different hydrogeomorphology and chemical characteristics. The morphological characteristics that distinguish these morphotypes varied gradually; besides, the morphotypes were randomly distributed. Conclusions. We conclude that Eunotia parasiolii is a species with a great morphological variability and wide distribution. We propose to emend the description of the species, since the original diagnosis does not include characteristics of the fine structure of the frustules and therefore is insufficient to differentiate it from its allied taxa.