Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial endophyte communities of two wheatgrass varieties following propagation in different growing media

Bacterial endophyte communities of two wheatgrass varieties currently being used in the revegetation of military training ranges were studied. Culturable and direct 16S rDNA PCR amplification techniques were used to describe bacterial communities present in Siberian and slender wheatgrass seeds, leaf tissues, and root tissues following propagation in either sand or a peat-based growing mix. Our hypothesis was that the resulting plant endophytic communities would be distinct, showing not only the presence of endophytes originating from the seed but also the characteristics of growth in the two different growing media. Both culture and culture-independent assays showed the likely translocation of Actinobacteria, Firmicutes, and Gammaproteobacteria from seed to mature plant tissues as well as subsequent colonization by exogenous organisms. Statistical analysis of 16S terminal restriction fragment profiles identified growing media as having a greater significant effect on the formation of the endpoint endophytic communities than either plant tissue or wheatgrass variety. In silico digests of the ribosomal database produced putative identifications indicating an increase in overall species diversity and increased relative abundances of Firmicutes and Cyanobacteria following propagation in sand and Betaproteobacteria following propagation in the peat-based growing mix. Results indicated a substantial translocation of endophytes from seed to mature plant tissues for both growing media and that growing medium was a dominant determinant of the final taxonomy of the endpoint plant endophytic communities.
Effects of dietary conjugated linoleic acid and fish oil supplementation on performance and egg quality in laying hens

1. Laying hen performance, yolk fat fatty acid concentrations and firmness of eggs were evaluated with respect to the inclusion in the diet of conjugated linoleic acid (CLA) and fish oil. 2. Nine diets were arranged factorially, with three levels of supplementation of CLA (1, 3 and 5 g/kg) and fish oil (0, 14 and 20 g/kg). 3. Type of diet did not affect egg production traits. 4. CLA addition increased yolk weight and yolk fat concentrations of CLA, saturated and total long-chain n-3 fatty acids, but decreased those of monounsaturated and total long-chain n-6 fatty acids. 5. Fish oil addition increased long-chain n-3 fatty acids yolk fat concentrations but decreased those of CLA, saturated and long-chain n-6 fatty acids. 6. Effects of CLA addition on yolk fat concentrations of C22:4 n-6 and C20:5 n-3 were greater when no fish oil was added to the diet. 7. CLA supplementation increased linearly yolk moisture and firmness and altered albumen and yolk pH.
Smart DC Power Management System Based on Software-Configurable Power Modules

DC bus-based systems are envisioned as an enabling technology to integrate renewable energy sources, energy storage devices, and a variety of loads in a number of power management and distribution scenarios. The system design and integration challenges include accommodating heterogeneous components, the wide variability of operating conditions, and system stability issues arising from dynamical interactions between the components. This paper proposes a flexible, smart dc power management architecture based on identical digitally controlled bidirectional dc–dc modules that can be software configured to enable simple system design, exceptional system flexibility, and optimization of the use of available resources. Design of the reconfigurable digital control infrastructure of such versatile dc power system is discussed in detail from its system-level description to the low-level design of the digital compensators. Stability analysis of the dc bus voltage is also discussed, proving the robustness of the power architecture from a theoretical standpoint. The proposed approach is then demonstrated on an experimental dc power management system consisting of several 500 W, bidirectional dc–dc modules operating from a 24-V dc bus.
Suitability of human and mammalian cells of different origin for the assessment of genotoxicity of metal and polymeric engineered nanoparticles

Abstract Nanogenotoxicity is a crucial endpoint in safety testing of nanomaterials as it addresses potential mutagenicity, which has implications for risks of both genetic disease and carcinogenesis. Within the NanoTEST project, we investigated the genotoxic potential of well-characterised nanoparticles (NPs): titanium dioxide (TiO2) NPs of nominal size 20 nm, iron oxide (8 nm) both uncoated (U-Fe3O4) and oleic acid coated (OC-Fe3O4), rhodamine-labelled amorphous silica 25 (Fl-25 SiO2) and 50 nm (Fl-50 SiO) and polylactic glycolic acid polyethylene oxide polymeric NPs – as well as Endorem® as a negative control for detection of strand breaks and oxidised DNA lesions with the alkaline comet assay. Using primary cells and cell lines derived from blood (human lymphocytes and lymphoblastoid TK6 cells), vascular/central nervous system (human endothelial human cerebral endothelial cells), liver (rat hepatocytes and Kupffer cells), kidney (monkey Cos-1 and human HEK293 cells), lung (human bronchial 16HBE14o cells) and placenta (human BeWo b30), we were interested in which in vitro cell model is sufficient to detect positive (genotoxic) and negative (non-genotoxic) responses. All in vitro studies were harmonized, i.e. NPs from the same batch, and identical dispersion protocols (for TiO2 NPs, two dispersions were used), exposure time, concentration range, culture conditions and time-courses were used. The results from the statistical evaluation show that OC-Fe3O4 and TiO2 NPs are genotoxic in the experimental conditions used. When all NPs were included in the analysis, no differences were seen among cell lines – demonstrating the usefulness of the assay in all cells to identify genotoxic and non-genotoxic NPs. The TK6 cells, human lymphocytes, BeWo b30 and kidney cells seem to be the most reliable for detecting a dose-response.
Prospective study of plasma homocysteine, its dietary determinants, and risk of age-related macular degeneration in men

ABSTRACT Purpose: Cross-sectional and case–control studies generally support a direct association between elevated plasma homocysteine and age-related macular degeneration (AMD), but data from prospective studies are limited. We examined the prospective relation of plasma homocysteine level, its dietary determinants, and risk of AMD in a large cohort of apparently healthy male physicians. Methods: During a mean follow-up of 11.2 years, we identified 146 incident cases of visually significant AMD (responsible for a reduction of visual acuity to 20/30 or worse), and 146 controls matched for age, smoking status, and time of blood draw. We measured concentration of homocysteine in blood samples collected at baseline using an enzymatic assay. and we assessed dietary intake of B vitamins and related compounds betaine and choline with a food frequency questionnaire administered at baseline. Results: AMD was not associated with plasma level of homocysteine; the multivariable-adjusted odds ratio (OR) of AMD comparing the highest and lowest quartile of homocysteine was 1.09 (95% confidence interval [95% CI]: 0.52–2.31; p for trend = 0.99). However, AMD was inversely associated with quartile of intake of total folate (OR: 0.55; 95% CI: 0.24–1.23; p for trend = 0.08), vitamin B6 from food (OR: 0.39; 95% CI: 0.17–0.88; p for trend = 0.01), and betaine (OR: 0.53; 95% CI: 0.22–1.27; p for trend = 0.048). Conclusions: These prospective data from a cohort of apparently healthy men do not support a major role for homocysteine in AMD occurrence, but do suggest a possible beneficial role for higher intake of several nutrients involved in homocysteine metabolism.
Changes in the MR relaxation rate R2* induced by respiratory challenges at 3.0 T: a comparison of two quantification methods

The consistent determination of changes in the transverse relaxation rate R2* (ΔR2*) is essential for the mapping of the effect of hyperoxic and hypercapnic respiratory challenges, which enables the noninvasive assessment of blood oxygenation changes and vasoreactivity by MRI. The purpose of this study was to compare the performance of two different methods of ΔR2* quantification from dynamic multigradient‐echo data: (A) subtraction of R2* values calculated from monoexponential decay functions; and (B) computation of ΔR2* echo‐wise from signal intensity ratios. A group of healthy volunteers (n = 12) was investigated at 3.0 T, and the brain tissue response to carbogen and CO2–air inhalation was registered using a dynamic multigradient‐echo sequence with high temporal and spatial resolution. Results of the ΔR2* quantification obtained by the two methods were compared with respect to the quality of the voxel‐wise ΔR2* response, the number of responding voxels and the behaviour of the ‘global’ response of all voxels with significant R2* changes. For the two ΔR2* quantification methods, we found no differences in the temporal variation of the voxel‐wise ΔR2* responses or in the detection sensitivity. The maximum change in the ‘global’ response was slightly smaller when ΔR2* was derived from signal intensity ratios. In conclusion, this first methodological comparison shows that both ΔR2* quantifications, from monoexponential approximation as well as from signal intensity ratios, are applicable for the monitoring of R2* changes during respiratory challenges. Copyright © 2010 John Wiley & Sons, Ltd.
Nitric oxide in patients with chronic liver diseases.

AIM Chronic liver disease (CLD) may be accompanied by portal hypertension (PHT). Nitric oxide (NO) system disturbances seem to play a key role in the pathogenesis of CLD and PHT. In this study we aim to assess if in chronic active hepatitis (CAH) and cirrhosis (CIR), CLD severity and etiology can be correlated with the serum level of NO metabolites. METHOD The study was performed on 92 patients divided according to the diagnosis and Child-Pugh class, and a control group of 10 healthy volunteers. Serum nitrite/nitrate and citrulline levels were measured in order to evaluate NO synthesis. RESULTS AND CONCLUSION In CLD patients there was an increased NO production. In CIR NO synthesis increased more than in CAH. In CIR patients only nitrite/nitrate concentrations were correlated with citrulline levels. NO metabolites from CAH and CIR patients varied according to disease etiology, namely NO synthesis was more important in HCV-CLD than in alcoholic-CLD and HBV-CLD. In CIR patients, NO metabolites level increased with disease severity.
Dysregulation of axonal sodium channel isoforms after adult‐onset chronic demyelination

Demyelination results in conduction block through changes in passive cable properties of an axon and in the expression and localization of axonal ion channels. We show here that adult‐onset chronic demyelination, such as occurs in demyelinating disorders and after nerve injury, alters the complement of axonal voltage‐dependent Na+ (Nav) channel isoforms and their localization. As a model, we used heterozygous transgenic mice with two extra copies of the proteolipid protein gene (Plp/−). Retinal ganglion cell axons in these mice myelinate normally, with young Plp/− and wild‐type mice expressing Nav1.2 at low levels, whereas Nav1.6 is clustered in high densities at nodes of Ranvier. At 7 months of age, however, Plp/− mice exhibit severe demyelination and oligodendrocyte cell death, leading to a profound reduction in Nav1.6 clusters, loss of the paranodal axoglial apparatus, and a marked increase in Nav1.2. We conclude that myelin is crucial not only for node of Ranvier formation, but also to actively maintain the proper localization and complement of distinct axonal Nav channel isoforms throughout life. The altered Nav channel isoform localization and complement induced by demyelination may contribute to the pathophysiology of demyelinating disorders and nerve injury. © 2003 Wiley‐Liss, Inc.
Aiolos Overexpression in Systemic Lupus Erythematosus B Cell Subtypes and BAFF-Induced Memory B Cell Differentiation Are Reduced by CC-220 Modulation of Cereblon Activity

BAFF is a B cell survival and maturation factor implicated in the pathogenesis of systemic lupus erythematosus (SLE). In this in vitro study, we describe that soluble BAFF in combination with IL-2 and IL-21 is a T cell contact-independent inducer of human B cell proliferation, plasmablast differentiation, and IgG secretion from circulating CD27+ memory and memory-like CD27−IgD− double-negative (DN) B cells, but not CD27−IgD+ naive B cells. In contrast, soluble CD40L in combination with IL-2 and IL-21 induces these activities in both memory and naive B cells. Blood from healthy donors and SLE patients have similar circulating levels of IL-2, whereas SLE patients exhibit elevated BAFF and DN B cells and reduced IL-21. B cell differentiation transcription factors in memory, DN, and naive B cells in SLE show elevated levels of Aiolos, whereas Ikaros levels are unchanged. Treatment with CC-220, a modulator of the cullin ring ligase 4-cereblon E3 ubiquitin ligase complex, reduces Aiolos and Ikaros protein levels and BAFF- and CD40L-induced proliferation, plasmablast differentiation, and IgG secretion. The observation that the soluble factors BAFF, IL-2, and IL-21 induce memory and DN B cell activation and differentiation has implications for extrafollicular plasmablast development within inflamed tissue. Inhibition of B cell plasmablast differentiation by reduction of Aiolos and Ikaros may have utility in the treatment of SLE, where elevated levels of BAFF and Aiolos may prime CD27+ memory and DN memory-like B cells to become Ab-producing plasmablasts in the presence of BAFF and proinflammatory cytokines.
The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease

Aging induces morphological changes of the kidney and reduces renal function. We analyzed the low molecular weight urinary proteome of 324 healthy individuals from 2–73 years of age to gain insight on human renal aging. We observed age‐related modification of secretion of 325 out of over 5000 urinary peptides. The majority of these changes were associated with renal development before and during puberty, while 49 peptides were related to aging in adults. We therefore focussed the remainder of the study on these 49 peptides. The majority of these 49 peptides were also markers of chronic kidney disease, suggesting high similarity between aging and chronic kidney disease. Blinded evaluation of samples from healthy volunteers and diabetic nephropathy patients confirmed both the correlation of biomarkers with aging and with renal disease. Identification of a number of these aging‐related peptides led us to hypothesize that reduced proteolytic activity is involved in human renal aging. Finally, among the 324 supposedly healthy individuals, some had urinary aging‐related peptide excretion patterns typical of an individual significantly older than their actual age. In conclusion, these aging‐related biomarkers may allow noninvasive detection of renal lesions in healthy persons and show high resemblance between human aging and chronic kidney disease. This similarity has to be taken into account when searching for biomarkers of renal disease.
Selective Use of Whole-Lung Irradiation for Patients With Ewing Sarcoma Family Tumors and Pulmonary Metastases at the Time of Diagnosis

Purpose The benefit of whole-lung irradiation (WLI) for patients who have pulmonary metastases (PM) of Ewing sarcoma family tumors (ESFT) is unclear. At our institution, WLI is reserved for patients with PM that do not respond completely to induction chemotherapy. We reviewed our experience to assess the impact of WLI on clinical outcome. Patients and Methods Twenty-eight patients with ESFT and PM were treated in three consecutive institutional trials (1979–1996). Extent of pulmonary involvement at diagnosis, response of PM after induction chemotherapy, local treatment of PM thereafter, and clinical outcome were recorded. Treatment included primary tumor surgery and/or radiotherapy and 42 to 58 weeks of multiagent chemotherapy. Results Only eight patients (29%) received WLI. For the entire study group, the estimated 5-year event-free survival was 22.9% ± 9.0%; the 5-year survival was 37.3% ± 9.8%. Complete resolution of PM after induction chemotherapy was not correlated with survival (P = 0.53), nor was treatment with WLI (P = 0.87). Conclusions The comparable survival of patients with poor and good response of PM to induction chemotherapy suggests that WLI may benefit poor responders. The use of WLI in good responders may provide similar benefit and merits further study.
Computation offloading game for an UAV network in mobile edge computing

Due to the limitations of mobile devices in terms of processing power and battery lifetime, cloud based solutions offer an attractive approach to answer these shortcomings. Since offloading intensive computation tasks to an edge/cloud server would achieve impressive performances, computation offloading paradigm has attracted the focus of many research groups in the last few years. This paper considers the problem of computation offloading while achieving a tradeoff between execution time and energy consumption. The proposed solution is intended for a fleet of small drones that are required to achieve highly intensive computation tasks. Drones need to detect, identify and classify objects or situations. Thus, they are brought to deal with intensive tasks such as pattern recognition and video preprocessing. The latter implement very complex calculations and typically require dedicated and powerful processors, which would definitely accentuate the dilemma between energy and delay. We adopted a game theory model where the players are all the drones in the network with three possible strategies. We defined the cost function to be minimized as a combination of energy overhead and delay. The simulation results are very promising and the achieved performances outperformed their counterparts in terms of average system wide cost and scalability.
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

Significance Outside of permafrost, no contiguous DNA sequences have been generated from material older than ∼120,000 y. By improving our ability to sequence very short DNA fragments, we have recovered the mitochondrial genome sequence of a >300,000-y-old cave bear from Sima de los Huesos, a Spanish cave site that is famous for its rich collection of Middle Pleistocene human fossils. This finding demonstrates that DNA can survive for hundreds of thousands of years outside of permafrost and opens the prospect of making more samples from this time period accessible to genetic studies. Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.
Calculation of pressure fields from arbitrarily shaped, apodized, and excited ultrasound transducers

A method for simulation of pulsed pressure fields from arbitrarily shaped, apodized and excited ultrasound transducers is suggested. It relies on the Tupholme-Stepanishen method for calculating pulsed pressure fields, and can also handle the continuous wave and pulse-echo case. The field is calculated by dividing the surface into small rectangles and then Summing their response. A fast calculation is obtained by using the far-field approximation. Examples of the accuracy of the approach and actual calculation times are given. <<ETX>>
Short-term Effect of Intravitreal Injection of Ranibizumab (Lucentis) on Intraocular Pressure

PurposeTo investigate short-term effect on intraocular pressure (IOP) after intravitreal injection of ranibizumab (Lucentis) (IVIL). Materials and MethodsThis prospective study included 1 eye of 54 patients (64±12 y) with wet age-related macular degeneration treated with IVIL. IOP measurements with TonoPen were taken: immediately before and 5 seconds, 5, 10, 15, 30, 60 minutes, and 1 day after IVIL. Axial length (with ultrasound biometry) was assessed in 24 eyes. The analysis included IOP difference at various time points and between phakic and pseudophakic eyes and the relationship between axial length and IOP increases after 5 seconds. ResultsMean IOP were 16.3±3.0 mm Hg (range: 12.0 to 21.3), 44.1±10.6 (22.0 to 59.3), 29.0±9.6 (15.0 to 49.0), 25.8±7.9 (16.0 to 45.0), 23.7±6.6 (15.7 to 39.0), 21.9±5.6 (14.7 to 37.0), 18.8±6.1 (10.0 to 35.0), and 16.1±3.0 (11.0 to 21.0), respectively, for time points immediately before, 5 seconds, 5, 10, 15, 30, 60 minutes, and 1 day after IVIL. Differences between before IVIL and after IVIL IOP were statistically significant after 5 seconds, 5, 10, 15, and 30 minutes (P=0.0001); however, were not significant after 1 hour (P=0.064) and 1 day (P=0.449). Differences between phakic and pseudophakic eyes were not significant (P>0.05). The relationship between shorter axial length and IOP increase after 5 seconds was significant (linear regression analysis; R2=0.28, P=0.007). ConclusionsIVIL causes a considerable short-term transient rise in IOP. The IOP increase after IVIL can be statistically significant at 0 to 30 minutes after injection in both phakic and pseudophakic eyes, and tends to be greater in shorter eyes.
N-Methyl-d-aspartate Inhibits Apoptosis through Activation of Phosphatidylinositol 3-Kinase in Cerebellar Granule Neurons

Primary cultured rat cerebellar granule neurons underwent apoptosis when switched from medium containing 25 mm K+ to one containing 5 mmK+. N-methyl-d-aspartate (NMDA) protected granule neurons from apoptosis in medium containing 5 mm K+. Inhibition of apoptosis by NMDA was blocked by the phosphatidylinositol 3-kinase (PI 3-kinase) inhibitor LY294002, but it was unaffected by the mitogen-activated protein kinase kinase inhibitor PD 98059. The antiapoptotic action of NMDA was associated with an increase in the tyrosine phosphorylation of insulin receptor substrate 1 (IRS-1), an increase in the binding of the regulatory subunit of PI 3-kinase to IRS-1, and a stimulation of PI 3-kinase activity. In the absence of extracellular Ca2+, NMDA was unable to prevent apoptosis or to phosphorylate IRS-1 and activate PI 3-kinase. Significant inhibition of NMDA-mediated neuronal survival by ethanol (10–15%) was observed at 1 mm, and inhibition was half-maximal at 45–50 mm. Inhibition of neuronal survival by ethanol corresponded with a marked reduction in the capacity of NMDA to increase the concentration of intracellular Ca2+, phosphorylate IRS-1, and activate PI 3-kinase. These data demonstrate that the neurotrophic action of NMDA and its inhibition by ethanol are mediated by alterations in the activity of a PI 3-kinase-dependent antiapoptotic signaling pathway.