Miracle-dz/UniFAR-FTUs huggingface dataset:
Francisella tularensis Glyceraldehyde-3-Phosphate Dehydrogenase Is Relocalized during Intracellular Infection and Reveals Effect on Cytokine Gene Expression and Signaling

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known for its multifunctionality in several pathogenic bacteria. Our previously reported data suggest that the GAPDH homologue of Francisella tularensis, GapA, might also be involved in other processes beyond metabolism. In the present study, we explored GapA’s potential implication in pathogenic processes at the host cell level. Using immunoelectron microscopy, we demonstrated the localization of this bacterial protein inside infected macrophages and its peripheral distribution in bacterial cells increasing with infection time. A quantitative proteomic approach based on stable isotope labeling of amino acids in cell culture (SILAC) combined with pull-down assay enabled the identification of several of GapA’s potential interacting partners within the host cell proteome. Two of these partners were further confirmed by alternative methods. We also investigated the impact of gapA deletion on the transcription of selected cytokine genes and the activation of the main signaling pathways. Our results show that ∆gapA-induced transcription of genes encoding several cytokines whose expressions were not affected in cells infected with a fully virulent wild-type strain. That might be caused, at least in part, by the detected differences in ERK/MAPK signaling activation. The experimental observations together demonstrate that the F. tularensis GAPDH homologue is directly implicated in multiple host cellular processes and, thereby, that it participates in several molecular mechanisms of pathogenesis.
First-principles study of the strain effect with half-metallic ferromagnetism in Cd 1−x V x Te alloys: supercell approaches

In this work, we study the effect of vanadium (V) dopantson the structural, electronic, and magnetic properties of the CdTe alloys using density functional theory (DFT). The calculations are performed as a function of the concentration of V in the host CdTe semiconductor using a 2 × 2 × 1 tetragonal supercell and a 2 × 2 × 2 cubic supercell. The lattice constants and bulk modulus of Cd 1−x V x Te alloys are determined. The analysis of the density of states shows that the Cd0.75 V0.25Te alloys in both supercells present a total polarization of 100% at the Fermi level, which confirms a stable half-metallic ferromagnetism phase in these materials, in contrast to the Cd 0.9375 V 0.0625 Te and Cd 0.875 V 0.125 Te alloys, which have a polarizability that does not reach 100%. In addition, the electronic band structures are used to estimate the s(p) − d exchange constants mainly resulting from the p − d hybridization between V- 3d and Te-p. Furthermore, the local magnetic moment of V of its free space charge value decreases, leading to the appearance of a small magnetic moment on the Cd and Te sites. Besides, the magnetic stability at different doping concentrations in the ferromagnetic (FM) and anti-ferromagnetic (AFM) states is examined, where the total energy of the systems is considered as a stability criterion. The robustness of the half-metallicity and the curie temperatures under the strain effect are also investigated. Finally, we rely on the binding energy to evaluate the energetic stability of the vanadium in the intrinsic compound CdTe under external deformations.
GERDA Status Report: Results from Commissioning

In June 2010 GERDA, designed to search for neutrinoless double beta decay of 76Ge, started the commissioning, with a pilot string of 3 non-enriched Ge detector. One year later 3 enrGedetectors were added, and operated for ∼ 4 months. This contribution summarizes the first year of work, the updated evaluation of the setup background, the strategies we implemented to mitigate the most serious background source we faced with, i.e. 42Ar-42K: the 42Ar activity measured in the final quasi-field free configuration is 0.23 ± 0.03 cts/(kg.d) corresponding to 104 Bq/kg; this is assuming an homogeneous and isotropic distribution of the daugther nucleus, 42K, around the detector array. The background index measured with the enrGe 3-detector array is 0.045+0.015−0.011 cts/(keV-kg-y).
Disruption of Coronal Magnetic Field Arcades

The ideal and resistive properties of isolated large-scale coronal magnetic arcades are studied using axisymmetric solutions of the time-dependent magnetohydrodynamic (MHD) equations in spherical geometry. We examine how flares and coronal mass ejections may be initiated by sudden disruptions of the magnetic field. The evolution of coronal arcades in response to applied shearing photospheric flows indicates that disruptive behavior can occur beyond a critical shear. The disruption can be traced to ideal MHD magnetic nonequilibrium. The magnetic field expands outward in a process that opens the field lines and produces a tangential discontinuity in the magnetic field. In the presence of plasma resistivity, the resulting current sheet is the site of rapid reconnection, leading to an impulsive release of magnetic energy, fast flows, and the ejection of a plasmoid. We relate these results to previous studies of force-free fields and to the properties of the open-field configuration. We show that the field lines in an arcade are forced open when the magnetic energy approaches (but is still below) the open-field energy, creating a partially open field in which most of the field lines extend away from the solar surface. Preliminary application of this model to helmet streamers indicates that it is relevant to the initiation of coronal mass ejections.
Planar waveguide spatial heterodyne spectrometer

Design and simulations of a Fourier-transform planar waveguide spectrometer are presented in the context of space-born observations of water in the near infrared spectral region. Spatial heterodyning of an optical signal is realized by using arrayed waveguide structures which produce spectrally dependent interference fringes. The light spectrum is calculated using discrete spatial Fourier transformation of the fringes. The arrayed waveguides form a multi-aperture input which markedly increases the optical throughput (étendue) of the device compared to single-aperture spectrometers.
The Relationship between Iron and LRRK2 in a 6-OHDA-Induced Parkinson’s Disease Model

The pathogenesis of Parkinson’s disease (PD) is very complex and still needs further exploration. Leucine-rich repeat kinase 2 (LRRK2) is associated with familial PD in mutant forms and sporadic PD in the wild-type form. Abnormal iron accumulation is found in the substantia nigra of PD patients, but its exact effects are not very clear. Here, we show that iron dextran exacerbates the neurological deficit and loss of dopaminergic neurons in 6-OHDA lesioned rats. 6-OHDA and ferric ammonium citrate (FAC) significantly increase the activity of LRRK2 as reflected by the phosphorylation of LRRK2, at S935 and S1292 sites. 6-OHDA-induced LRRK2 phosphorylation is attenuated by the iron chelator deferoxamine, especially at the S1292 site. 6-OHDA and FAC markedly induce the expression of pro-apoptotic molecules and the production of ROS by activating LRRK2. Furthermore, G2019S-LRRK2 with high kinase activity showed the strongest absorptive capacity for ferrous iron and the highest intracellular iron content among WT-LRRK2, G2019S-LRRK2, and kinase-inactive D2017A-LRRK2 groups. Taken together, our results demonstrate that iron promotes the activation of LRRK2, and active LRRK2 accelerates ferrous iron uptake, suggesting that there exists an interplay between iron and LRRK2 in dopaminergic neurons, providing a new perspective to uncover the underlying mechanisms of PD occurrence.
3-D eigenmode calculation of metallic nano-structures

Abstract. In the calculation of eigenfrequencies of 3-D metallic nanostructures occurs the challenge that the material parameters depend on the desired eigenfrequency. We propose a formulation where this leads to a polynomial eigenvalue problem which can be tackled by different solving strategies. A comparison between a Newton-type method and a Jacobi-Davidson algorithm is given.
Scanning capacitance microscopy

A novel mechanically scanned and non-contacting surface profiling instrument has been developed in which a fine wire probe is raster scanned over the surface of the sample under examination. Measurement of the modulated capacitance between the probe and the vibrated sample is used to maintain the probe just above the surface. In the prototype instrument described, an in-plane resolution better than 2 mu m is achieved by the use of an etched tungsten wire probe, while the perpendicular resolution is 6 nm. Both insulating and conducting samples may be scanned and the technique makes it possible to measure electrical properties of the surface under the probe as well as the surface microtopography.
New lithium observations of two (Fe/H) = -3.5 or less dwarfs

We report new lithium observations for the extremely metal-poor main-sequence turnoff stars CS 22876-32 and CS 29527-15. High signal-to-noise echelle spectra show a 11 mA feature at λ6707 for the brighter component of the double-lined spectroscopic binary CS 22876-32. With a magnitude difference estimated at 1.2 mag and a velocity shift of 28 km s −1 between components, its inferred logarithmic lithium abundance is N(Li)=12+log(Li/H)=2.02±0.18, which is consistent with the Spite plateau abundance 2.10±0.10. However, CS 29527-15, with an estimated [Fe/H]=−3.4 and T eff =6250 K, shows no lithium feature at a 3 σ detection limit of 10 mA
Inhibition of Tetrahymena pyriformis growth by Aliphatic Alcohols and Amines: a QSAR Study

A Quantitative Structure- Activity Relationship (QSAR) study was undertaken to evaluate the relative toxicity of a mixed series of 21 (linear and branched-chain) alcohols and 9 normal aliphatic amines in term of the 50% inhibitory growth concentration (IGC50) of Tetrahymena pyriformis. The applied simple linear regression approach is based on theoretical 3D (geometrical ) molecular descriptors from DRAGON package, and some calculated logP descriptors. The robustness and the predictive performance of the models were verified using both internal (cross-validation by LOO and LMO; bootstrap) and external statistical validations. ClogP turned out to be the best descriptor to model the considered endpoint. It may be interchanged with geometrical descriptor ADDD without relevant variations in the statistical parameters. Keywords: Alcohols and Amines –Aquatic toxicity – QSAR – Geometrical descriptors and hydrophobic character – Simple linear regression Une etude Relation Quantitative Structure- Activite (QSAR) a ete realisee pour evaluer la toxicite relative d’un melange compose de 21 alcools (a chaines lineaires et ramifiees) et 9 amines aliphatiques normales, en terme de concentration d’inhibition 50% de la croissance (IGC50) de Tetrahymena pyriformis . L’approche par regression lineaire simple est basee sur des descripteurs moleculaires theoriques (geometriques) 3D obtenus a l’aide du logiciel DRAGON et differents descripteurs logP calcules. La robustesse et la capacite predictive des modeles ont ete verifiees a l’aide de statistiques de validations internes (validations croisees LOO et LMO ; bootstrap) et externe. Clog s’est avere le meilleur descripteur pour la modelisation de la grandeur d’interet consideree. Il peut etre remplace par le descripteur geometrique ADDD sans variations appreciables des parametres statistiques. Mots cles: Alcools et Amines – Toxicite aquatique – QSAR – Descripteurs geometriques et caractere hydrophobe – Regression lineaire simple.
Relationship of iodine excess with thyroid function in 6-year-old children living in an iodine-replete area

Background Adequate iodine intake is essential for growing children, as both deficient and excessive iodine status can result in thyroid dysfunction. We investigated the iodine status and its association with thyroid function in 6-year-old children from South Korea. Methods A total of 439 children aged 6 (231 boys and 208 girls) were investigated from the Environment and Development of Children cohort study. The thyroid function test included free thyroxine (FT4), total triiodothyronine (T3), and thyroid-stimulating hormone (TSH). Urine iodine status was evaluated using urine iodine concentration (UIC) in morning spot urine and categorized into iodine deficient (< 100 μg/L), adequate (100–199 μg/L), more than adequate (200–299 μg/L), mild excessive (300–999 μg/L), and severe excessive (≥ 1000 μg/L) groups. The estimated 24-hour urinary iodine excretion (24h-UIE) was also calculated. Results The median TSH level was 2.3 μIU/mL, with subclinical hypothyroidism detected in 4.3% of patients without sex differences. The median UIC was 606.2 μg/L, with higher levels in boys (684 μg/L vs. 545 μg/L, p = 0.021) than girls. Iodine status was categorized as deficient (n = 19, 4.3%), adequate (n = 42, 9.6%), more than adequate (n = 54, 12.3%), mild excessive (n = 170, 38.7%), or severe excessive (n = 154, 35.1%). After adjusting for age, sex, birth weight, gestational age, body mass index z-score, and family history, both the mild and severe excess groups showed lower FT4 (β = − 0.04, p = 0.032 for mild excess; β = − 0.04, p = 0.042 for severe excess) and T3 levels (β = − 8.12, p = 0.009 for mild excess; β = − 9.08, p = 0.004 for severe excess) compared to the adequate group. Log-transformed estimated 24h-UIE showed a positive association with log-transformed TSH levels (β = 0.04, p = 0.046). Conclusion Excess iodine was prevalent (73.8%) in 6-year-old Korean children. Excess iodine was associated with a decrease in FT4 or T3 levels and an increase in TSH levels. The longitudinal effects of iodine excess on later thyroid function and health outcomes require further investigation.
Free Energy Methods for Efficient Exploration of Mixture Posterior Densities

Because of their multimodality, mixture posterior densities are difficult to sample withstandard Markov chain Monte Carlo (MCMC) methods. We propose a strategy to enhancethe sampling of MCMC in this context, using a biasing procedure which originates fromcomputational statistical physics. The principle is first to choose a "reaction coordinate",that is, a direction in which the target density is multimodal. In a second step, the marginallog-density of the reaction coordinate is estimated; this quantity is called "free energy" inthe computational statistical physics literature. To this end, we use adaptive biasing Markovchain algorithms which adapt their invariant distribution on the fly, in order to overcomesampling barriers along the chosen reaction coordinate. Finally, we perform an importancesampling step in order to remove the bias and recover the true posterior. The efficiency factorcan easily be estimated a priori once the bias is known, and is large enough for the test caseswe considered.A crucial point is the choice of the reaction coordinate. One standard choice (used forexample in the classical Wang-Landau algorithm) is the opposite of the log-posterior density.We show that another convenient and efficient reaction coordinate is the hyper-parameterthat determines the order of magnitude of the variance of each component. We also showhow to adapt the method to perform model choice between different number of components.We illustrate our approach by analyzing two real data sets.
Molecular conformation during steady‐state measurements of extensional viscosity

Recent measurements by Tirtaatmadja and Sridhar (1993) of extensional viscosity of polymer solutions show that a steady state was reached in some cases. Since their test fluids were dilute or nearly dilute solutions, and since the strains were as high as seven by the end of the uniaxial stretching, it is supposed that the polymer chains were fully extended. Two analyses are carried out to investigate whether this assumed conformation of the linear macromolecules is consistent with the conditions observed at steady state. The first analysis uses Batchelor’s formula for a suspension of elongated particles to estimate the steady‐state values of extensional viscosity. Values calculated from the formula are about an order of magnitude higher than the experimental ones, which suggests that the chains were not fully extended at steady state. The second analysis predicts the strain necessary to completely unfold a randomly coiled chain. The analysis is based on a new lower‐bound equation and on prior simulations .
A Method for Combined PassiveActive Microwave Retrievals of Cloud and Precipitation Profiles

Abstract Three-dimensional tropical squall-line simulations from the Goddard cumulus ensemble (GCE) model are used as input to radiative computations of upwelling microwave brightness temperatures and radar reflectivities at selected microwave sensor frequencies. These cloud/radiative calculations form the basis of a physical cloud/precipitation profile retrieval method that yields estimates of the expected values of the hydrometeor water contents. Application of the retrieval method to simulated nadir-view observations of the aircraft-borne Advanced Microwave Precipitation Radiometer (AMPR) and NASA ER-2 Doppler radar (EDOP) produce random errors of 23%, 19%, and 53% in instantaneous estimates of integrated precipitating liquid, integrated precipitating ice, and surface rain rate, respectively. On 5 October 1993, during the Convection and Atmospheric Moisture Experiment (CAMEX), the AMPR and EDOP were used to observe convective systems in the vicinity of the Florida peninsula. Although the AMPR data alon.
Identification of TSGA10 and GGNBP2 splicing variants in 5′ untranslated region with distinct expression profiles in brain tumor samples

Introduction Brain tumors (BTs) are perceived as one of the most common malignancies among children. The specific regulation of each gene can play a critical role in cancer progression. The present study aimed to determine the transcripts of the TSGA10 and GGNBP2 genes, considering the alternative 5′UTR region, and investigating the expression of these different transcripts in BTs. Material and methods Public data on brain tumor microarray datasets in GEO were analyzed with R software to evaluate the expression levels of TSGA10 and GGNBP2 genes (the Pheatmap package in R was also used to plot DEGs in a heat map). In addition, to validate our in-silico data analysis, RT-PCR was performed to determine the splicing variants of TSGA10 and GGNBP2 genes in testis and brain tumor samples. The expression levels of splice variants of these genes were analyzed in 30 brain tumor samples and two testicular tissue samples as a positive control. Results In silico results show that the differential expression levels of TSGA10 and GGNBP2 were significant in the GEO datasets of BTs compared to normal samples (with adjusted p-value<0.05 and log fold change > 1). This study’s experimental results showed that the TSGA10 gene produces four different transcripts with two distinct promoter regions and splicing exon 4. The relative mRNA expression of transcripts without exon 4 was higher than transcripts with exon 4 in BT samples (p-value<001). In GGNBP2, exon 2 in the 5′UTR region and exon 6 in the coding sequence were spliced. The expression analysis results showed that the relative mRNA expression of transcript variants without exon 2 was higher than other transcript variants with exon 2 in BT samples (p-value<001). Conclusion The decreased expression levels of transcripts with longer 5′UTR in BT samples than in testicular or low-grade brain tumor samples may decrease their translation efficiency. Therefore, decreased amounts of TSGA10 and GGNBP2 as potential tumor suppressor proteins, especially in high-grade brain tumors, may cause cancer development by angiogenesis and metastasis.
A New Advanced Class of Convex Functions with Related Results

It is the purpose of this paper to propose a novel class of convex functions associated with strong η-convexity. A relationship between the newly defined function and an earlier generalized class of convex functions is hereby established. To point out the importance of the new class of functions, some examples are presented. Additionally, the famous Hermite–Hadamard inequality is derived for this generalized family of convex functions. Furthermore, some inequalities and results for strong η-convex function are also derived. We anticipate that this new class of convex functions will open the research door to more investigations in this direction.
Gene Drive: Past, Present and Future Roads to Vertebrate Biocontrol

Scientists have long sought a technology to humanely control populations of damaging invasive pests in a species-specific manner. Gene drive technology could see this become a reality. This review charts the twists and turns on the road to developing gene drives in vertebrates. We focus on rodents, as these will likely be the first targets, and trace the journey from the early understanding of selfish genetic elements to engineering gene drives in mice; before discussing future research focuses and the crucial role that public perception and governance will play in the application of this technology. The realisation of robust gene drive strategies in vertebrate pests has the potential to revolutionise biocontrol.
Implications of changes in land use on soil and biomass carbon sequestration: a case study from the Owabi reservoir catchment in Ghana

Abstract Land use changes affect soil and biomass carbon sequestration potential of the agroecosystems of most Sub-Sahara Africa facing rising temperatures due to global climate change. One such ecosystem is the Owabi reservoir catchment in Ghana, which has undergone extensive changes in land use through urbanization. Our study aimed to determine the impact of the spatial and temporal variability of the different land uses on soil and biomass carbon storage in the Owabi catchment. Land use/cover maps were elaborated using SPOT satellite images of 30 × 30-m resolution and Erdas Imagine and ArcGIS Pro softwares. Soil and vegetation were sampled along three transects in the Y plane in early 2014. Nested plot design and temporary sample plots of 50 × 50 m were demarcated within a 1 ha plot in each of the land uses. Trees, herbs and litter were sampled to assess aboveground carbon, and soil samples were taken at 0–15 cm and 15–30 cm depth. Belowground (root) biomass was calculated using the root:shoot ratio. Seven (7) land use types – dense forest, sparse forest, grassland, cropland, wetland, settlement, and excavated land – were identified and differences in carbon stocks were assessed. Soil carbon stock (0–30 cm) ranged from 51.80 Mg/ha in dense forest to 7.00 Mg/ha in excavated land. Our study showed that the conversion of forest lands to other land uses through excavation resulted in about 30-folds loss in carbon and also a major loss of carbon in the catchment from c. 1.4 × 106 Mg C in 1990 to 0.55 × 106 Mg C in 2014. Enhancing forests or growing trees to sequester carbon seems to be the optimum choice among the seven land uses if the introduction of payment for environmental services options is considered.