Miracle-dz/UniFAR-FTUs huggingface dataset:
The dichroism and birefringence of a hard‐sphere suspension under shear

Optical measurements were used to detect structural anisotropy in concentrated dispersions over a range of Peclet numbers. Silica spheres of 49 and 130 nm radii with grafted octadecyl chains were dispersed in cyclohexane at volume fractions from 0.1 to 0.4. The apparatus consisted of a Couette cell with the dispersion in the annulus probed by a HeNe laser beam parallel to the axis of rotation. The dichroism and birefringence of the transmitted beam varied linearly with shear rate at low Peclet numbers with an orientation coincident with the principle direction of shear. Increasing the Peclet number, by increasing the particle size, produced a nonlinear response with the orientation tending to align in the direction of flow. A theory coupling the nonequilibrium microstructure under shear to the optical properties of the suspension enables direct interpretation of the dichroism. Comparison of sample dichroism calculations for two different forms of the theory demonstrates that the optical technique can be u.
Copper phthalocyanine layer as an organic semiconductor sensor of NO2 in air

Abstract The applicability of copper phthalocyanine (CuPc) as an organic semiconductor gas sensor for the detection of high concentrations of NO2 in air is the aim of this study. Thin films of CuPc were deposited by sublimation. Measurements were carried out to determine the effect of NO2 on the conductivity of a CuPc film. A detection method for NO2 in air is proposed.
Dissolved organic nitrogen and carbon in pastoral soils: the New Zealand experience

Dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soils are increasingly recognized as important components of nutrient cycling and biological processes in soil‐plant ecosystems. The aims of this study were to: (i) quantify the pools of DON and DOC in a range of New Zealand pastoral soils; (ii) compare the effects of land use changes on these pools; and (iii) examine the seasonal variability associated with these two components of dissolved organic matter. Soil samples (0–7.5 cm depth) from 93 pastoral sites located in Northland, Waikato, Bay of Plenty and Otago/Southland, New Zealand, were collected in autumn. Adjacent sites under long‐term arable cropping or native vegetation and forestry land use were also sampled at the same time to estimate the impacts of different land use on DON and DOC in these soils. Twelve dairy and 12 sheep and or beef pastures were sampled in winter, spring, summer and autumn for a 2‐year period to study the seasonal fluctuations of DON and DOC. A field incubation study was also carried out in a grazed pasture to examine fluctuations in the concentrations of and and DON levels in soil. Other soil biological properties, such as microbial biomass‐C, biomass‐N and mineralizable N, were also measured. Pastoral soils contained the greatest amounts of DON (13–93 mg N kg−1 soil, equivalent to 8–55 kg N ha−1) and DOC (73–718 mg C kg−1 soil, equivalent to 44–431 kg C ha−1), followed by cropping and native vegetation and forestry soils. The DON concentration in soils was found to be more seasonally variable than DOC. There was approximately 80% fluctuation in the concentration of DON in winter from the annual mean concentration of DON, while DOC fluctuated between 23 and 28% at the dairy and the sheep and beef monitoring sites. Similar fluctuations in the concentrations of DON were also observed in the field incubation studies. These results indicate that DON is a dynamic pool of N in soils. There was a strong and significant positive correlation between DON and DOC in pastoral soils (r = 0.71, P < 0.01). There were also significant positive correlations between DON and total soil C (r = 0.59, P < 0.01), total soil N (r = 0.62, P < 0.01) and mineralizable N (r = 0.47, P < 0.01). The rather poor correlations between total soil C and N with DOC and DON, suggest other biogeochemical processes may be influencing concentrations of DOC and DON in these soils. Given the size of DON and DOC pools in the pastoral soils, we suggest that these pools of C and N should be taken into account when assessing the impact of pastoral land use on soil C and N enrichment of surface and groundwater.
Wetting properties of AFM probes by means of contact angle measurement

An atomic force microscopy (AFM) based technique was developed to measure the wetting properties of probe tips. By advancing and receding the AFM tip across the water surface, the meniscus force between the tip and the liquid was measured at the tip–water separation. The water contact angle was determined from the meniscus force. The obtained contact angle results were compared with that by the sessile drop method. It was found that the AFM based technique provided higher contact angle values than the sessile drop method. The mechanisms responsible for the difference are discussed.
Effect of Nature and Particle Size on Properties of Uniform Magnetite and Maghemite Nanoparticles

Magnetite nanoparticles with two different sizes, 5 and 17 nm, have been prepared by the decomposition of organic precursors in an organic media in the presence of oleic acid. The particles were characterized by TEM, X-ray diffraction, and IR and Mossbauer spectroscopy to clarify their structural and physicochemical properties. The samples consist of noninteracting magnetite nanoparticles in both cases with a more uniform size distribution and higher crystal order degree than particles of similar sizes prepared by coprecipitation. A controlled heat treatment of the samples in air leads to the transformation of magnetite to maghemite, which can be followed by the appearance of many IR bands forbidden for a spinel structure. In addition to that, an important reduction of saturation magnetization and coercivity at low temperature takes place whenever the oleic acid is preserved. Finally, Mossbauer spectra at different temperatures clearly show the effect of the nature of the iron oxide phase, the particle si.
Low-Frequency Dielectric Relaxations in Nematics and Dual-Frequency Addressing of Field Effects

Abstract Novel low threshold nematic mixtures are presented exhibiting very low dielectric crossover frequencies fc ≃ 1 kHz at 20°C and unusually large, low- as well as high-frequency dielectric anisotropies ΔEL > 4 and ΔEH < 4 respectively. ΔEL and ΔEH are shown to be independently adjustable. The frequency and temperature dependence of the dielectric constants as well as the optical, elastic and viscous material constants are measured. Approximations are derived which quantitatively describe the influence of the LC material properties on the static electro-optical performance of dual-frequency addressed twisted nematic displays. It is shown that the number of multiplexable lines of dual-frequency addressed TN-LCDs comprising the new materials can be increased by more than a factor of 30 compared with conventional addressing. Moreover, very short turn-off times are reported.
CARBON-TO-NITROGEN RATIO AND HYDRAULIC RETENTION TIME EFFECT ON THE ANAEROBIC DIGESTION OF CHEESE WHEY.

ABSTRACT SIXTEEN 1-L digesters were used to test four carbon-to-nitrogen ratios of 8.4, 13.9, 22.2 and 27.6 and four hydraulic retention times of 12, 18, 24 and 30 days on the efficiency of digester operation. Percent methane in the biogas and methane production were dependent on both carbon-to-nitrogen ratio and hydraulic retention times. Percent chemical oxygen demand reduction, volatile solids removal, total volatile acids concentrations, digester pH and amount of sodium hydroxide solution needed to control digester pH were dependent on hydraulic retention time only.
Myricitrin, a Glycosyloxyflavone in Myrica esculenta Bark Ameliorates Diabetic Nephropathy via Improving Glycemic Status, Reducing Oxidative Stress, and Suppressing Inflammation

The present study evaluated the therapeutic potential of myricitrin (Myr), a glycosyloxyflavone extracted from Myrica esculenta bark, against diabetic nephropathy. Myr exhibited a significant hypoglycemic effect in high fat-fed and a single low-dose streptozotocin-induced type 2 diabetic (T2D) rats. Myr was found to improve glucose uptake by the skeletal muscle via activating IRS-1/PI3K/Akt/GLUT4 signaling in vitro and in vivo. Myr significantly attenuated high glucose (HG)-induced toxicity in NRK cells and in the kidneys of T2D rats. In this study, hyperglycemia caused nephrotoxicity via endorsing oxidative stress and inflammation resulting in the induction of apoptosis, fibrosis, and inflammatory damages. Myr was found to attenuate oxidative stress via scavenging/neutralizing oxidative radicals and improving endogenous redox defense through Nrf-2 activation in both in vitro and in vivo systems. Myr was also found to attenuate diabetes-triggered renal inflammation via suppressing NF-κB activation. Myr inhibited hyperglycemia-induced apoptosis and fibrosis in renal cells evidenced by the changes in the expressions of the apoptotic and fibrotic factors. The molecular docking predicted the interactions between Myr and different signal proteins. An in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) study predicted the drug-likeness character of Myr. Results suggested the possibility of Myr to be a potential therapeutic agent for diabetic nephropathy in the future.
Tumor Mutational Burden Is Polygenic and Genetically Associated with Complex Traits and Diseases

This study provides evidence for a polygenic architecture of tumor mutational burden and opens an avenue for the use of whole-genome germline genetic variations to stratify patients with cancer for immunotherapy. Tumor mutational burden (TMB) is an emerging biomarker of response to immunotherapy in solid tumors. However, the extent to which variation in TMB between patients is attributable to germline genetic variation remains elusive. Here, using 7,004 unrelated patients of European descent across 33 cancer types from The Cancer Genome Atlas, we show that pan-cancer TMB is polygenic with approximately 13% of its variation explained by approximately 1.1 million common variants altogether. We identify germline variants that affect TMB in stomach adenocarcinoma through altering the expression levels of BAG5 and KLC1. Further analyses provide evidence that TMB is genetically associated with complex traits and diseases, such as smoking, rheumatoid arthritis, height, and cancers, and some of the associations are likely causal. Overall, these results provide new insights into the genetic basis of somatic mutations in tumors and may inform future efforts to use genetic variants to stratify patients for immunotherapy. Significance: This study provides evidence for a polygenic architecture of tumor mutational burden and opens an avenue for the use of whole-genome germline genetic variations to stratify patients with cancer for immunotherapy.
Comparing Clinician-Assessed and Patient-Reported Performance Status for Predicting Morbidity and Mortality in Patients With Advanced Cancer Receiving Chemotherapy.

PURPOSE Performance status (PS) is assessed during cancer treatment to determine clinical trial eligibility, appropriateness for treatment, and need for supportive care. There is rising interest for patients to report this information directly. We determined whether clinician- and patient-reported PS were equally associated with mortality and service utilization in patients with cancer. METHODS A secondary analysis was conducted using data from an radiotherapy plus chemotherapy in which 441 patients with advanced cancer and clinicians reported PS using the Eastern Cooperative Oncology Group scale. Simple kappa statistics measured agreement between clinician-reported performance status (cPS) and patient-reported performance status (pPS). Associations of cPS and pPS with emergency department (ED) and hospital visits and overall survival were evaluated via Cox regression, competing risk regression, and Fisher's exact tests. RESULTS cPS and pPS correlated weakly (kappa = 0.27). Both pPS and cPS were associated with survival, ED visits, and hospitalizations, but only cPS remained associated after adjustment (survival: HR, 1.75; P < .0001). The first available cPS predicted mortality more strongly than the first available pPS (HR for death, comparing PS ≥ 1 v 0: 2.05 for cPS and 1.41 for pPS). When pPS questionnaires were repeated over time and averaged, associations with outcomes were stronger as measured by AIC model fit. Both pPS and cPS were associated with EQ-5D subcomponents (eg, 75%-77% with no usual activity deficits for PS 0, v 42%-51% for PS ≥ 1). CONCLUSION Both clinician-reported PS and patient-reported PS provide useful information and can be considered for clinical trials and routine care.
Higher Sensitivity of Soil Microbial Network Than Community Structure under Acid Rain

Acid rain (AR), as a global environmental threat, has profoundly adverse effects on natural soil ecosystems. Microorganisms involved in the nitrogen (N) cycle regulate the global N balance and climate stabilization, but little is known whether and how AR influences the structure and complexity of these microbial communities. Herein, we conducted an intact soil core experiment by manipulating the acidity of simulated rain (pH 7.5 (control, CK) vs. pH 4.0 (AR)) in subtropical agricultural soil, to reveal the differences in the structure and complexity of soil nitrifying and denitrifying microbiota using Illumina amplicon sequencing of functional genes (amoA, nirS, and nosZ). Networks of ammonia-oxidizing archaea (AOA) and nirS-carrying denitrifiers in AR treatment were less complex with fewer nodes and lower connectivity, while network of nosZ-carrying denitrifiers in AR treatment had higher complexity and connectivity relative to CK. Supporting this, AR reduced the abundance of keystone taxa in networks of AOA and nirS-carrying denitrifiers, but increased the abundance of keystone taxa in nosZ-carrying denitrifiers network. However, AR did not alter the community structure of AOA, ammonia-oxidizing bacteria (AOB), nirS-, and nosZ-carrying denitrifiers. Moreover, AR did not change soil N2O emissions during the experimental period. AOB community structure significantly correlated with content of soil available phosphorus (P), while the community structures of nirS- and nosZ-carrying denitrifiers both correlated with soil pH and available P content. Soil N2O emission was mainly driven by the nirS-carrying denitrifiers. Our results present new perspective on the impacts of AR on soil N-cycle microbial network complexity and keystone taxa in the context of global changes.
Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle

MicroRNAs (miRNAs) are key regulators of gene expression, potentially affecting several biological processes, whose function can be altered by sequence variation. Hence, the integration of single nucleotide polymorphisms (SNP) and miRNAs can explain individual differences in economic traits. To provide new insights into the effects of SNPs on miRNAs and their related target genes, we carried out a multi-omic analysis to identify SNPs in miRNA mature sequences (miR-SNPs) associated with fatty acid (FA) composition in the Nelore cattle. As a result, we identified 3 miR-SNPs in different miRNAs (bta-miR-2419-3p, bta-miR-193a-2, and bta-miR-1291) significantly associated with FA traits (p-value < 0.02, Bonferroni corrected). Among these, the rs110817643C>T, located in the seed sequence of the bta-miR-1291, was associated with different ω6 FAs, polyunsaturated FA, and polyunsaturated:saturated FA ratios. Concerning the other two miR-SNPs, the rs43400521T>C (located in the bta-miR-2419-3p) was associated with C12:0 and C18:1 cis-11 FA, whereas the rs516857374A>G (located in the bta-miR-193a-2) was associated with C18:3 ω6 and ratio of ω6/ω3 traits. Additionally, to identify potential biomarkers for FA composition, we described target genes affected by these miR-SNPs at the mRNA or protein level. Our multi-omics analysis outlines the effects of genetic polymorphism on miRNA, and it highlights miR-SNPs and target candidate genes that control beef fatty acid composition.
Atrial Fibrillation in Patients Undergoing Allogeneic Hematopoietic Cell Transplantation

PURPOSE To examine the incidence and risk factors for de novo atrial fibrillation (AF) after allogeneic hematopoietic cell transplantation (HCT) and to describe the impact of AF on HCT-related outcomes. METHODS A retrospective cohort study design was used to examine AF and associated outcomes in 487 patients who underwent allogeneic HCT from 2014 to 2016 and to characterize patient- and HCT-related risk factors. A nested case-control study design was used to describe the association between pre-HCT echocardiographic measures and future AF events. RESULTS The median age at HCT was 52.4 years (18.1-78.6); the median time to AF was 117.5 days (4.0-1,405.0). The 5-year cumulative incidence of AF was 10.6%. Older (≥ 50 years) age (hazard ratio [HR], 2.76; 95% CI, 1.37 to 5.58), HLA-unrelated donor (HR, 2.20; 95% CI, 1.18 to 4.12), dyslipidemia (HR, 2.40; 95% CI, 1.23 to 4.68), and pre-HCT prolonged QTc interval (HR, 2.55; 95% CI, 1.38 to 4.72) were independent risk factors for AF. Despite having comparable left ventricular systolic function, patients who developed AF were significantly more likely to have lower left atrial ejection fraction, left atrial reservoir function, and elevated tricuspid regurgitant jet velocity prior to HCT, compared with patients who did not. The incidence rate of stroke after AF was 143 per 1,000 person-years. In adjusted analyses, AF was associated with a 12.8-fold (HR, 12.76; 95% CI, 8.76 to 18.57) risk of all-cause mortality and 15.8-fold (HR, 15.78; 95% CI, 8.70 to 28.62) risk of nonrelapse mortality. CONCLUSION The burden of AF after allogeneic HCT population is substantial, and the development of AF is associated with poor survival. We identified important associations between patient demographics, pre-HCT cardiac parameters, HCT-related exposures, and risk of AF, setting the stage for targeted prevention strategies during and after HCT.
Salinity, Temperature and Ammonia Acute Stress Response in Seabream (Sparus aurata) Juveniles: A Multidisciplinary Study

Simple Summary Gilthead seabream (Sparus aurata) is a teleost fish of great relevance in marine aquaculture, especially in the Mediterranean area and one of the most important farmed food marine species in Europe. Nevertheless, in captivity fish are usually exposed to stressful conditions, with a consequent negative impact on animal welfare and growth. The principal goal of this study was to shed light on the acute stress response of gilthead seabream juveniles exposed to different stressors using a multidisciplinary approach. For this purpose, gilthead seabream have been exposed to three different stress tests (temperature, salinity, and ammonia changes) and several laboratory techniques have been used to evaluate their growth and stress response. Results revealed that all the tested stressors had an impact on fish growth and health, particularly thermic and chemical exposure, whereas salinity seems to have a minor effect since this species can efficiently face with extreme variations in environmental salinity. The present work aimed to obtain relevant information on acute stress response of gilthead seabream to be used for improving farming condition and ensuring fish welfare. Abstract The present study aimed to investigate the acute response of gilthead seabream (Sparus aurata) juveniles exposed to temperature, salinity and ammonia stress. Radioimmunoassay was used to evaluate cortisol levels, whereas insulin-like growth factors (igf1 and igf2), myostatin (mstn), heat-shock protein 70 (hsp70) and glucocorticoid receptor (gr) gene expression was assessed trough Real-Time PCR. The presence and localization of IGF-I and HSP70 were investigated by immunohistochemistry. In all the stress conditions, a significant increase in cortisol levels was observed reaching higher values in the thermic and chemical stress groups. Regarding fish growth markers, igf1 gene expression was significantly higher only in fish subjected to heat shock stress while, at 60 min, igf2 gene expression was significantly lower in all the stressed groups. Temperature and ammonia changes resulted in a higher mstn gene expression. Molecular analyses on stress response evidenced a time dependent increase in hsp70 gene expression, that was significantly higher at 60 min in fish exposed to heat shock and chemical stress. Furthermore, the same experimental groups were characterized by a significantly higher gr gene expression respect to the control one. Immunostaining for IGF-I and HSP70 antibodies was observed in skin, gills, liver, and digestive system of gilthead seabream juveniles.
The Highly Conservative Cysteine of Oncomodulin as a Feasible Redox Sensor

Oncomodulin (Ocm), or parvalbumin β, is an 11–12 kDa Ca2+-binding protein found inside and outside of vertebrate cells, which regulates numerous processes via poorly understood mechanisms. Ocm consists of two active Ca2+-specific domains of the EF-hand type (“helix-loop-helix” motif), covered by an EF-hand domain with inactive EF-hand loop, which contains a highly conservative cysteine with unknown function. In this study, we have explored peculiarities of the microenvironment of the conservative Cys18 of recombinant rat Ocm (rWT Ocm), redox properties of this residue, and structural/functional sensitivity of rWT Ocm to the homologous C18S substitution. We have found that pKa of the Cys18 thiol lays beyond the physiological pH range. The measurement of redox dependence of rWT Ocm thiol–disulfide equilibrium (glutathione redox pair) showed that redox potential of Cys18 for the metal-free and Ca2+-loaded protein is of −168 mV and −176 mV, respectively. Therefore, the conservative thiol of rWT Ocm is prone to disulfide dimerization under physiological redox conditions. The C18S substitution drastically reduces α-helices content of the metal-free and Mg2+-bound Ocm, increases solvent accessibility of its hydrophobic residues, eliminates the cooperative thermal transition in the apo-protein, suppresses Ca2+/Mg2+ affinity of the EF site, and accelerates Ca2+ dissociation from Ocm. The distinct structural and functional consequences of the minor structural modification of Cys18 indicate its possible redox sensory function. Since some other EF-hand proteins also contain a conservative redox-sensitive cysteine located in an inactive EF-hand loop, it is reasonable to suggest that in the course of evolution, some of the EF-hands attained redox sensitivity at the expense of the loss of their Ca2+ affinity.