Miracle-dz/UniFAR-FTUs huggingface dataset:
Does IRAS 16293–2422 have a hot core? Chemical inventory and abundance changes in its protostellar environment

A detailed radiative transfer analysis of the observed continuum and molecular line emission toward the deeply embedded young stellar object IRAS 16293-2422 is performed. Accurate molecular abundances and abundance changes with radius are presented. The continuum modelling is used to constrain the temperature and density distributions in the envelope, enabling quantitative estimates of various molecular abundances. The density structure is well described by a single power-law falling off as r^(-1.7), i.e., in the range of values predicted by infall models. A detailed analysis of the molecular line emission strengthens the adopted physical model and lends further support that parts of the circumstellar surroundings of IRAS are in a state of collapse. The molecular excitation analysis reveals that the emission from some molecular species is well reproduced assuming a constant fractional abundance throughout the envelope. The abundances and isotope ratios are generally close to typical values found in cold molecular clouds in these cases, and there is a high degree of deuterium fractionation. There are, however, a number of notable exceptions. Lines covering a wide range of excitation conditions indicate for some molecules, e.g., H_2CO, CH_3OH, SO, SO_2 and OCS, a drastic increase in their abundances in the warm and dense inner region of the circumstellar envelope. The location at which this increase occurs is consistent with the radius at which ices are expected to thermally evaporate off the grains. In all, there is strong evidence for the presence of a "hot core" close to the protostar, whose physical properties are similar to those detected towards most high mass protostars except for a scaling factor. However, the small scale of the hot gas and the infalling nature of the envelope lead to very different chemical time scales between low mass and high mass hot cores, such that only very rapidly produced second-generation complex molecules can be formed in IRAS 16293-2422 . Alternatively, the ices may be liberated due to grain-grain collisions in turbulent shear zones where the outflow interacts with the envelope. Higher angular resolution observations are needed to pinpoint the origin of the abundance enhancements and distinguish these two scenarios. The accurate molecular abundances presented for this low-mass protostar serve as a reference for comparison with other objects, in particular circumstellar disks and comets.
Origin and Evolution of the Bartonella Gene Transfer Agent

&NA; Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector‐borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage‐derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.
The Chromatin Structure of the Dual c-myc Promoter P1/P2 Is Regulated by Separate Elements*

The proto-oncogene c-myc is transcribed from a dual promoter P1/P2, with transcription initiation sites 160 base pairs apart. Here we have studied the transcriptional activation of both promoters on chromatin templates. c-mycchromatin was reconstituted on stably transfected, episomal, Epstein-Barr virus-derived vectors in a B cell line. Episomal P1 and P2 promoters showed only basal activity but were strongly inducible by histone deacetylase inhibitors. The effect of promoter mutations on c-myc activity, chromatin structure, and E2F binding was studied. The ME1a1 binding site between P1 and P2 was required for the maintenance of an open chromatin configuration of the dual c-myc promoters. Mutation of this site strongly reduced the sensitivity of the core promoter region of P1/P2 to micrococcal nuclease and prevented binding of polymerase II (pol II) at the P2 promoter. In contrast, mutation of the P2 TATA box also abolished binding of pol II at the P2 promoter but did not affect the chromatin structure of the P1/P2 core promoter region. The E2F binding site adjacent to ME1a1 is required for repression of the P2 promoter but not the P1 promoter, likely by recruitment of histone deacetylase activity. Chromatin precipitation experiments with E2F-specific antibodies revealed binding of E2F-1, E2F-2, and E2F-4 to the E2F site of the c-myc promoter in vivo if the E2F site was intact. Taken together, the analyses support a model with a functional hierarchy for regulatory elements in the c-mycpromoter region; binding of proteins to the ME1a1 site provides a nucleosome-free region of chromatin near the P2 start site, binding of E2F results in transcriptional repression without affecting polymerase recruitment, and the TATA box is required for polymerase recruitment.
Posttraumatic Growth in Parents After a Natural Disaster

Posttraumatic growth (PTG) was examined in Norwegian parents 2.5 years after they were exposed, together with their children, to the 2004 Southeast Asian tsunami. Parents reported on their own and their children's disaster exposure and posttraumatic stress symptoms (PTSS) 10 months post-disaster. Children reported their own PTSS. Multiple regression analyses showed that children's distress 10 months post-disaster predicted parental PTG 1 year later, over and above the effects of parents’ own distress and disaster exposure. This study demonstrates that stress and vulnerability related to parenting in and after a disaster situation may contribute to PTG.
Comparative genetic variance and heritability of head and facial traits in northwest Indian and Belgian twins

Genetic variance analysis of 13 head and facial traits is considered in samples of Northwest, Indian and Belgian twins. Modified t tests, based on the nested structure of twin data, indicate differences between monozygotic (MZ) and dizygotic (DZ) mean values of bigonial diameter in Indian females and in Belgian males, i.e., for only two of 52 instances. Heterogeneity of variance is observed in about 30% of the craniofacial traits in both samples, invalidating conventional within‐pair genetic variance estimates for these traits. Patterns of environmental bias on zygosities differ between sexes within the same population and also between the two samples. Revised average genetic variance ratios are higher in Indian than in Belgian twins. Male twins manifest, on average, higher genetic variance ratios than female twins in both the samples. There is stronger evidence of enviornmental covariance in MZ than in DZ twins for both Indian and Belgian twins. The pattern of intraclass corrlations, based on average values, is as follows: ♂rMZ > ♀rMZ > ♂rDZ ≥ ♀rDZ in the Indian twins and ♂rMZ > ♀rMZ > ♀rDZ > ♂rDZ in the Belgian twins.
Using conflict resolution to inform decentralized learning

Learning consistent policies in decentralized settings is often problematic. The agents have a myopic view of their neighboring states that could lead to inconsistent action choices. The fundamental question addressed in this work is how to determine and obtain the minimal overlapping context among decentralized decision makers required to make their decisions more consistent. Our approach is a two-phased learning process where agents first learn their policies offline within the context of a simplified environment where it is not necessary to know detailed context information about neighbors. These local policies are then applied in more complex "real" environments where it is expected that agents will encounter a much higher rate of inconsistencies (conflicts) with neighborhood actions. When conflicts are observed, agents switch to "special" states that augment local policy states with additional non-local state information and learn other actions to take in this specific situation. This results in action choices that are less likely to lead to conflicts. We evaluate our approach by addressing meta-level decisions in a complex multiagent weather tracking domain. Experimental results show that our approach achieves good performance on utility and conflict resolution by exploring only a small fraction of the whole search space.
A Review of Pain Assessment in Pigs

There is a moral obligation to minimize pain in pigs used for human benefit. In livestock production, pigs experience pain caused by management procedures, e.g., castration and tail docking, injuries from fighting or poor housing conditions, “management diseases” like mastitis or streptococcal meningitis, and at parturition. Pigs used in biomedical research undergo procedures that are regarded as painful in humans, but do not receive similar levels of analgesia, and pet pigs also experience potentially painful conditions. In all contexts, accurate pain assessment is a prerequisite in (a) the estimation of the welfare consequences of noxious interventions and (b) the development of more effective pain mitigation strategies. This narrative review identifies the sources of pain in pigs, discusses the various assessment measures currently available, and proposes directions for future investigation.
Analysis of process of emulsions transport in hydrophilic/oleophilic granular porous media driven by capillary force

The research focuses on the issues concerning a process of multiphase liquids transport in granular porous media driven by the capillary pressure. The current publication is meant to introduce the results of experimental research conducted to evaluate the kinetics of the imbibition and emulsions behavior inside the porous structures. Moreover, the influence of the dispersed phase concentration and granular media structure on the mentioned process was considered. The medium imbibition with emulsifier-stabilized emulsions composed of oil as the dispersed phase in concentrations of 10 vol%, 30 vol%, and 50 vol%, was investigated. The porous media consisted of oleophilic/hydrophilic beads with a fraction of 200–300 and 600–800 μm. The experimental results provided that the emulsions imbibition in such media depended stronger on its structure compare to single-phase liquids. The increase of the dispersed phase concentration caused an insignificant mass decreasing of the imbibed emulsions and height of its penetration in a sorptive medium. The concentrations of the imbibed dispersions exceeded their initial values, but reduced with permeants front raise in the granular structures that can be defined as the influential factor for wicking process kinetics. Symbols: As – cross-section area of a porous medium, m, Df – pore fractal dimension, -, db – average diameter of beads in a granular medium, m, dt – diameter of a tube, m, fn – fragment of a porous medium, m, hc – height of a liquid front in a capillary, m, him – imbibed liquid height, m, hm – height of a porous medium, m, hmax – maximal height of an imbibed liquid, m, mim – imbibed liquid mass, kg, Ls – distance in the flow direction, m, K – proportionality coefficient, m, kkc – Kozerny constant, -, rav – average pore radius of the investigated porous medium, m, rc – radius of a capillary, m, rh – hydraulic radius, m, rmax – maximum pore radius, m, rp – radius of pore, m, Sin – initial saturation, -, Sim – medium saturation after imbibition, m, tim – time of imbibition, s, φd – initial dispersed phase concentration, vol%, φim – dispersed phase concentration of an imbibed emulsion, vol%, ε – porosity of a medium, -, ρ – density of a wetting liquid, kg/m, δ – pore shape parameters, -,
Pulmonary arterial compliance in dogs and pigs : the three-element windkessel model revisited

PATRICK SEGERS,1 SERGE BRIMIOULLE,2 NIKOS STERGIOPULOS,3 NICO WESTERHOF,4 ROBERT NAEIJE,2 MARCO MAGGIORINI,2 AND PASCAL VERDONCK1 1Hydraulics Laboratory, Institute for Biomedical Technology, University of Gent, B-9000 Ghent, Belgium; 2Laboratory for Physiology, Free University of Brussels, B-1070 Brussels, Belgium; 3Biomedical Engineering Laboratory, École Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland; and 4Laboratory for Physiology, Institute for Cardiovascular Research, Free University of Amsterdam, 1081 BT Amsterdam, The Netherlands
Metabolic Flexibility of Sulfate-Reducing Bacteria

Dissimilatory sulfate-reducing prokaryotes (SRB) are a very diverse group of anaerobic bacteria that are omnipresent in nature and play an imperative role in the global cycling of carbon and sulfur. In anoxic marine sediments sulfate reduction accounts for up to 50% of the entire organic mineralization in coastal and shelf ecosystems where sulfate diffuses several meters deep into the sediment. As a consequence, SRB would be expected in the sulfate-containing upper sediment layers, whereas methanogenic archaea would be expected to succeed in the deeper sulfate-depleted layers of the sediment. Where sediments are high in organic matter, sulfate is depleted at shallow sediment depths, and biogenic methane production will occur. In the absence of sulfate, many SRB ferment organic acids and alcohols, producing hydrogen, acetate, and carbon dioxide, and may even rely on hydrogen- and acetate-scavenging methanogens to convert organic compounds to methane. SRB can establish two different life styles, and these can be termed as sulfidogenic and acetogenic, hydrogenogenic metabolism. The advantage of having different metabolic capabilities is that it raises the chance of survival in environments when electron acceptors become depleted. In marine sediments, SRB and methanogens do not compete but rather complement each other in the degradation of organic matter. Also in freshwater ecosystems with sulfate concentrations of only 10–200 μM, sulfate is consumed efficiently within the top several cm of the sediments. Here, many of the δ-Proteobacteria present have the genetic machinery to perform dissimilatory sulfate reduction, yet they have an acetogenic, hydrogenogenic way of life. In this review we evaluate the physiology and metabolic mode of SRB in relation with their environment.
Design and statistical optimization of glipizide loaded lipospheres using response surface methodology

Design and statistical optimization of glipizide loaded lipospheres using response surface methodology A 32 factorial design was employed to produce glipizide lipospheres by the emulsification phase separation technique using paraffin wax and stearic acid as retardants. The effect of critical formulation variables, namely levels of paraffin wax (X1) and proportion of stearic acid in the wax (X2) on geometric mean diameter (dg), percent encapsulation efficiency (% EE), release at the end of 12 h (rel12) and time taken for 50% of drug release (t50), were evaluated using the F-test. Mathematical models containing only the significant terms were generated for each response parameter using the multiple linear regression analysis (MLRA) and analysis of variance (ANOVA). Both formulation variables studied exerted a significant influence (p < 0.05) on the response parameters. Numerical optimization using the desirability approach was employed to develop an optimized formulation by setting constraints on the dependent and independent variables. The experimental values of dg, % EE, rel12 and t50 values for the optimized formulation were found to be 57.54 ± 1.38 μm, 86.28 ± 1.32%, 77.23 ± 2.78% and 5.60 ± 0.32 h, respectively, which were in close agreement with those predicted by the mathematical models. The drug release from lipospheres followed first-order kinetics and was characterized by the Higuchi diffusion model. The optimized liposphere formulation developed was found to produce sustained anti-diabetic activity following oral administration in rats. Dizaj i statistička optimizacija liposfera s glipizidom pomoću metodologije odgovora površine 32 faktorijalni dizajn je primijenjen za pripravu liposfera s glipizidom metodom separacije pomoću emulzija koristeći parafinski vosak i stearinsku kiselinu kao tvari za usporavanje. Pomoću F-testa praćen je učinak kritičnih varijabli tijekom formuliranja, tj. količina parafinskog voska (X1) i udio stearinske kiseline (X2) na srednji promjer liposfera (dg), postotak inkapsulirane ljekovite tvari (% EE), oslobađanje ljekovite tvari nakon 12 h (rel12) te vrijeme potrebno za oslobađanje 50% ljekovite tvari (t50). Za svaki parametar su pomoću multiple linearne regresijske analize (MLRA) i analize varijabli (ANOVA) načinjeni matematički modeli koji sadrže samo značajne varijable. Proučavanje varijabli na oba načina ukazalo je na njihov značajan utjecaj (p < 0,05) na parametre liposfera. Postavljanjem ograničenja na zavisne i nezavisne varijable provedena je numerička optimizacija na principu poželjnosti. Eksperimentalne vrijednosti dg, % EE, rel12 i t50 optimiziranih formulacija bile su 57,54 ± 1,38 μm, 86,28 ± 1,32%, 77,23 ± 2,78% i 5,60 ± 0,32 h. Dobivene eksperimentalne vrijednosti bile su vrlo slične vrijednostima predviđenim matematič kim modelima. Oslobađanje glipizida iz liposfera slijedio je kinetiku prvog reda i karakteriziran je Higuchijevim difuzijskim modelom. Optimizirane liposfere su nakon peroralne primjene na štakorima pokazale produljeni antidijabetički učinak.
Savannah: mobile gaming and learning?

This paper reports a study that attempts to explore how using mobile technologies in direct physical interaction with space and with other players can be combined with principles of engagement and self-motivation to create a powerful and engaging learning experience. We developed a mobile gaming experience designed to encourage the development of children's conceptual understanding of animal behaviour. Ten children (five boys and five girls) aged between 11 and 12 years played and explored the game. The findings from this study offer interesting insights into the extent to which mobile gaming might be employed as a tool for supporting learning. It also highlights a number of major challenges that this format raises for the organisation of learning within schools and the design of such resources.
An All-or-None Response in the Release of Potassium by Yeast Cells Treated with Methylene Blue and Other Basic Redox Dyes

Basic redox dyes, such as methylene blue, induce a loss of K+ from yeast cells. The maximal loss, rather than the rate of loss, is related to the dye concentration, the response following a normal distribution on a plot of log-dose, versus percentage loss of K+. This fact taken together with the observed correlation between K+ loss and frequency of staining (as measured by microscopic observation), indicates that the response is all-or-none for individual cells. The response is produced by all the basic redox dyes tested (9), but by none of the acidic dyes (4). However, only the oxidized form of the dye is effective. Cations protect the cells from the basic dyes in a competitive manner, the bivalent cations (especially UO2 ++) being more effective than monovalent cations. It is suggested that the action of the dyes involves two steps, the first a binding to ribonucleic acid in the cell membrane (with competition from cations) and the second, an oxidation of neighboring sulfhydryl groups to the disulfide form. At a threshold level, unique for each cell, a generalized membrane breakdown occurs, resulting in the release of potassium and of other cytoplasmic constituents.
Fluid Reabsorption and Glucose Consumption in Edematous Rat Lungs

Solute and water uptake were studied in isolated perfused rat lungs with airspaces filled with the perfusion fluid. The albumin in this solution was labelled with Evans blue (T-1824), and uptake of fluid from the airspaces was documented by an increase in T-1824 concentration in airway fluid of 6.5 ± 1.6% (n = 5, SEM) at 1 hour and 12.2 ± 0.9% (n = 10) at 2 hours. The only detectable osmotic force that could have contributed to a loss of fluid from the alveolar fluid was a decrease in airspace glucose concentrations, which fell much more rapidly (from 150 mg/dl to 58.7 ± 7.1 mg/dl, n = 10, after 2 hours) than plasma glucose (from 150 mg/dl to 128.9 ± 3.7 mg/dl). Addition of 5 ± 10−5 M terbutaline to the perfusate and airspace solutions nearly doubled fluid reabsorption at 1 hour, an effect that was inhibited by propranolol and did not appear to be related to glucose consumption. Exposure to terbutaline for 2 hours increased epithelial permeability to 3H-mannitol and 22Na+. These observations suggest that active sodium transport and epithelial metabolism or transport of glucose in airway fluid may each play a role in the reabsorption of edema fluid.
Trauma of the Frontal Region Is Influenced by the Volume of Frontal Sinuses. A Finite Element Study

Anatomy of frontal sinuses varies individually, from differences in volume and shape to a rare case when the sinuses are absent. However, there are scarce data related to influence of these variations on impact generated fracture pattern. Therefore, the aim of this study was to analyse the influence of frontal sinus volume on the stress distribution and fracture pattern in the frontal region. The study included four representative Finite Element models of the skull. Reference model was built on the basis of computed tomography scans of a human head with normally developed frontal sinuses. By modifying the reference model, three additional models were generated: a model without sinuses, with hypoplasic, and with hyperplasic sinuses. A 7.7 kN force was applied perpendicularly to the forehead of each model, in order to simulate a frontal impact. The results demonstrated that the distribution of impact stress in frontal region depends on the frontal sinus volume. The anterior sinus wall showed the highest fragility in case with hyperplasic sinuses, whereas posterior wall/inner plate showed more fragility in cases with hypoplasic and undeveloped sinuses. Well-developed frontal sinuses might, through absorption of the impact energy by anterior wall, protect the posterior wall and intracranial contents.