Miracle-dz/UniFAR-FTUs huggingface dataset:
Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort.

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1(T), was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27(T), Methylobacterium fujisawaense DSM 5686(T), Methylobacterium radiotolerans JCM 2831(T) and Methylobacterium jeotgali S2R03-9(T), with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA-DNA relatedness between strain JT1(T) and these and the type strains of other closely related species were lower than 70 %. Cells of JT1(T) stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm(-2)). Major fatty acids were C(18 : 1)ω7c and C(16 : 0). Based on the morphological, physiological and biochemical data presented, strain JT1(T) is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1(T) ( = DSM 21328(T) = CCUG 56108(T)).
Modulation of Heart Fibroblast Migration and Collagen Gel Contraction by IGF-I

Dynamic interactions between cells and the extracellular matrix are essential in the regulation of a number of cellular processes including migration, adhesion, proliferation and differentiation. A variety of factors have been identified which modulate these interactions including transforming growth factor+, platelet-derived growth factor and others. Insulin-like growth factors have been shown to regulate collagen production by heart fibroblasts; however, the effects of this growth factor on the interactions of heart fibroblasts with the extracellular matrix have not been examined. The present studies were carried out to determine the effects of IGF-I on the ability of fibroblasts to interact with the extracellular matrix and to begin to determine the mechanisms of this response. These experiments illustrate that IGF-I treatment results in increased migration, collagen reorganization and gel contraction by heart fibroblasts. IGF-I has been shown to activate both the mitogen-activated protein kinase and phophatidylinositol-3 kinase pathways in isolated cells. Experiments with pharmacological antagonists of these pathways indicate that the mitogen-activated protein kinase pathway is essential for IGF-I stimulated collagen gel contraction by fibroblasts. These studies illustrate that IGF-I modulates the ability of fibroblasts to interact with the collagen matrix and that activation of multiple signaling pathways by IGF-I may produce distinct downstream responses in these cells.
Domination Game: A proof of the 3/5-Conjecture for Graphs with Minimum Degree at Least Two

In the domination game on a graph $G$, the players Dominator and Staller alternately select vertices of $G$. Each vertex chosen must strictly increase the number of vertices dominated. This process eventually produces a dominating set of $G$; Dominator aims to minimize the size of this set, while Staller aims to maximize it. The size of the dominating set produced under optimal play is the game domination number of $G$, denoted by $\gamma_g (G)$. In this paper, we prove that $\gamma_g(G) \le 2n/3$ for every $n$-vertex isolate-free graph $G$. When $G$ has minimum degree at least $2$, we prove the stronger bound $\gamma_g(G) \le 3n/5$; this resolves a special case of a conjecture due to Kinnersley, West, and Zamani [SIAM J. Discrete Math., 27 (2013), pp. 2090--2107]. Finally, we prove that if $G$ is an $n$-vertex isolate-free graph with $\ell$ vertices of degree 1, then $\gamma_g(G) \le 3n/5 + \left \lceil \ell/2 \right \rceil + 1$; in the course of establishing this result, we answer a question of Bresar e.
Matching of Shapes Bound by Freeform Curves

AbstractMatching and retrieval of shapes, both in two and three dimensions, have been a topic of interest to researchers in the field of computer graphics, vision and geometric modeling for at least a decade. In this paper, a shape is assumed to be represented as set of freeform curved boundaries. A prominent approach to matching curved outline is the graph-based approach, where a skeleton is used as a basis for obtaining the graph. In general, graph-matching is a hard problem and the comparison costs increase proportionally with graph size and hence slows down the process. In this paper, the skeleton, and in particular, medial axis of curved boundaries has been used. As opposed to using graph-based matching, statistical-based methods of signatures obtained from the properties of the skeleton have been employed. This enables a faster construction of shape signatures thereby increasing the speed of matching. Moreover, this facilitates the comparison of shapes that may have the presence of holes (inner loop.
Evidence for the involvement of histaminergic neurones in the regulation of the rat oxytocinergic system during pregnancy and parturition

1 Previous studies have shown that histaminergic neurones of the tuberomammillary nucleus project directly to hypothalamic magnocellular nuclei and that intracerebroventricular administration of histamine increases the synthetic activity of magnocellular oxytocin neurones. 2 Histaminergic neurones of the dorsomedial tuberomammillary nucleus that project to the magnocellular region of the paraventricular nucleus are activated during late pregnancy and lactation, as measured by an increase in mRNA for the synthetic enzyme histidine decarboxylase. 3 There is a concomitant increase in oxytocin mRNA in magnocellular neurones of the paraventricular nucleus. This increase in mRNA contributes to an accumulation of oxytocin before birth and to continued oxytocin synthesis during lactation. 4 Intracerebroventricular administration of mepyramine, a specific antagonist of the H1histamine receptor, causes a delay in the birth of subsequent pups if given to the mother during parturition. Vehicle or the H2 receptor antagonist cimetidine has no effect. Thus, histamine acts centrally, via H1 receptors, during parturition and may have an excitatory effect on oxytocin release. 5 These results suggest that afferent histaminergic neurones show increased activity during pregnancy and may be responsible for the increase of synthesis in magnocellular oxytocin neurones at this time. If, as previously reported, these histamine neurones can reduce the electrical activity of oxytocin neurones via H2 receptors, then they may have a dual effect, increasing the synthesis of oxytocin while inhibiting its premature release. At term, any inhibitory effects of histamine are overcome to allow oxytocin secretion.
GENOMIC SELECTION : THE FUTURE OF MARKER ASSISTED SELECTION AND ANIMAL BREEDING

Marker-Assisted-Selection (MAS) is mainly important in situations, where the current accuracy of selection is low, e.g. traits with low heritability, limited, late-in-life, or afterslaughter recording. In veloand whizzo genetics schemes, the number of selection cycles per time period is minimized, which may increase rates of genetic gain dramatically. Genomic selection is used to obtain a high accuracy of selection of in-uturo calves or early embryos.
Improved method for hot embossing As2S3 waveguides employing a thermally stable chalcogenide coating.

We demonstrate the fabrication of As2S3 rib waveguides using hot embossing. Because of the high temperature required, a thin (50nm) Ge(11.5)As(24)Se(64.5) was thermally evaporated on top of an 870nm As(2)S(3) layer to protect against surface degradation during embossing. The waveguides propagation loss was 0.52dB/cm for the TE and 0.41dB/cm for the TM polarizations at 1550nm for a waveguide cross-section dimension of 3.8 × 1μm. The nonlinearity of a 2. 2μm wide waveguide was shown to be 13500W(-1)km(-1) using four-wave mixing demonstrating that these embossed waveguides were capable of being used for all-optical processing.
Screening and Predicting Posttraumatic Stress and Depression in Children Following Single-Incident Trauma

Three screening methods to predict posttraumatic stress disorder (PTSD) and depression symptoms in children following single-incident trauma were tested. Children and adolescents (N = 90; aged 7–17 years) were assessed within 4 weeks of an injury that led to hospital treatment and followed up 3 and 6 months later. Screening methods were adapted from existing instruments and examined (a) an Australian version of the Screening Tool for Predictors of PTSD (STEPP-AUS), (b) an abbreviated measure of initial PTSD severity, and (c) an abbreviated measure of initial maladaptive trauma-specific beliefs. The STEPP-AUS correctly identified 89% of the children who developed PTSD at 6-month follow-up and the 69% of children who were non-PTSD. Predictive performance of the others instruments was generally poor, and no instrument consistently predicted subclinical levels of depression.
Screening for HIV. U.S. Preventive Services task Force.

RECOMMENDATION Screening for infection with human immunodeficiency virus should be offered periodically to persons seeking treatment for sexually transmitted diseases, intravenous drug users, homosexual and bisexual men, and other at increased risk of infection. Testing should also be offered to pregnant women (or women contemplating pregnancy) who are at increased risk for HIV infection. Testing should not be performed in the absence of informed consent and adequate pretest and post-test counseling. Clinicians should be careful to use proper tests and qualified laboratories. Seropositive persons require adequate post-test counseling, and drug and sexual partners should be properly notified. Persons with negative test results also require counseling and repeat testing when appropriate.
Multiple classification without model order estimation

A novel approach to weighting eigen-subspaces is proposed which leads to a pseudo-spectrum with super-resolution performance similar to the MUSIC algorithm without the need for model-order detection. The method is shown to be applicable to a type of problem encountered in active carrier-wave sonar direction of arrival estimation where the SNR is high and the targets are discrete point targets and few in number. The method forms a covariance matrix with subsequent eigendecomposition as in MUSIC. Similarly, a pseudo-spectrum is formed as a reciprocal of a weighted reconstruction. Weights are used for all eigenvectors, contrasting with MUSIC & weighted subspace methods which typically use only the noise subspace. Further the weights proposed here include functions based on the nature of each individual eigenvector which can be related to the sparsity of the components of the eigenvector. The presented results of digital simulation demonstrate a performance comparable to MUSIC & MUSIC + MDL for a range of signal/target positions, relative strengths & SNR values. Further, application of the algorithm to the real sonar data shows promising improvement in target localisation.
FhuA Barrel-Cork Hybrids Are Active Transporters and Receptors

ABSTRACT The crystal structure of Escherichia coli FhuA reveals a β-barrel domain that is closed by a globular cork domain. It has been assumed that the proton motive force of the cytoplasmic membrane through the interaction of the TonB protein with the TonB box of the cork opens the FhuA channel. Yet, deletion of the cork results in an FhuA derivative, FhuAΔ5–160, that still displays TonB-dependent substrate transport and phage receptor activity. To investigate this unexpected finding further, we constructed FhuAΔ5–160 derivatives of FhuA proteins from Salmonella paratyphi B, Salmonella enterica serovar Typhimurium, and Pantoea agglomerans. The FhuAΔ5–160 proteins inserted correctly into the outer membrane, and with the exception of the P. agglomerans protein, transported ferrichrome and albomycin. FhuA hybrids consisting of the β-barrel of one strain and the cork of another strain were active and showed higher TonB-dependent ferrichrome transport rates than the corkless derivatives. Exceptions were theE. coli β-barrel/Salmonella serovar Typhimurium cork hybrid protein and the Salmonella serovar Typhimurium β-barrel/P. agglomerans cork hybrid protein, both of which were less active than the β-barrels alone. Each of the FhuA mutant proteins displayed activity for each of their ligands, except for phage T5, only when coupled to TonB. The hybrid FhuA proteins displayed a similar activity with the E. coli TonB protein as with their cognate TonB proteins. Sensitivity to phages T1, T5, and φ80, rifamycin CGP 4832, and colicin M was determined by the β-barrel, whereas sensitivity to phage ES18 and microcin J25 required both the β-barrel and cork domains. These results demonstrate that the β-barrel domain of FhuA confers activity and specificity and responds to TonB and that the cork domains of various FhuA proteins can be interchanged and contribute to the activities of the FhuA hybrids.
Modulation of bandgap and current in Graphene/BN heterostructures by tuning the transverse electric field

By means of atomistic Tight Binding simulations, we study heterostructures made of an armchair BN nanoribbon sided by two armchair graphene ribbons where a high band gap can be opened. We show that this band gap can be significantly suppressed by applying a relatively weak transverse electric field. This effect can be used to strongly enhance the on/off current ratio higher in graphene transistors.
Automatic Intra-Subject Registration-Based Segmentation of Abdominal Fat From Three-Dimensional Water – Fat MRI

Materials and Methods: Data were obtained from 11 subjects at two time points with intermediate repositioning, and from four subjects before and after a meal with repositioning. Imaging was performed on a 3 Tesla MRI, using the IDEAL chemical-shift water–fat pulse sequence. Adipose tissue (subcutaneous—SAT, visceral—VAT) and organs (liver, pancreas) were manually segmented twice for each scan by a single trained observer. Automated segmentations of each subject’s second scan were generated using a nonrigid volume registration algorithm for water–fat MRI images that used a b-spline basis for deformation and minimized image dissimilarity after the deformation. Manual and automated segmentations were compared using Dice coefficients and linear regression of SAT and VAT volumes, organ volumes, and hepatic and pancreatic fat fractions (HFF, PFF).
NOTCH1 Up-regulation and Signaling Involved in Mycobacterium bovis BCG-induced SOCS3 Expression in Macrophages*

Suppressor of cytokine signaling (SOCS) 3 is a critical negative regulator of cytokine signaling and is induced by Mycobacterium bovis Bacille Calmette-Guérin (M. bovis BCG) in mouse macrophages. However, little is known about the early receptor proximal signaling mechanisms underlying mycobacteria-mediated induction of SOCS3. We demonstrate here for the first time that M. bovis BCG up-regulates NOTCH1 and activates the NOTCH1 signaling pathway, leading to the expression of SOCS3. We show that perturbing Notch signaling in infected macrophages results in the marked reduction in the expression of SOCS3. Furthermore, enforced expression of the Notch1 intracellular domain in RAW 264.7 macrophages induces the expression of SOCS3, which can be further potentiated by M. bovis BCG. The perturbation of Toll-like receptor (TLR) 2 signaling resulted in marked reduction in SOCS3 levels and expression of the NOTCH1 target gene, Hes1. The down-regulation of MyD88 resulted in a significant decrease in SOCS3 expression, implicating the role of the TLR2-MyD88 axis in M. bovis BCG-triggered signaling. However, the SOCS3 inducing ability of M. bovis BCG remains unaltered also upon infection of macrophages from TLR4-defective C3H/HeJ mice. More importantly, signaling perturbation data suggest the involvement of cross-talk among members of the phosphoinositide 3-kinase and mitogen-activated protein kinase cascades with NOTCH1 signaling in SOCS3 expression. Furthermore, SOCS3 expression requires the NOTCH1-mediated recruitment of Suppressor of Hairless (CSL) and nuclear factor-κBtothe Socs3 promoter. Overall, these results implicate NOTCH1 signaling during inducible expression of SOCS3 following infection of macrophages with an intracellular bacillus-like M. bovis BCG.
Electrochemical impedimetric sensing of nitrate contamination in water

This paper describes the design and development of a sensing system to detect the nitrate concentration by using planar interdigital sensor immersed in the water sample. Water samples were prepared containing two different salts: Sodium Nitrate (NaNO3) and Ammonium Nitrate (NH4NO3) with the concentration ranging from 0.02 PPM to 10 PPM by using the serial dilution method. The water sample was tested by both the commercial equipment (LCR meter) and designed system. Although a difference was observed between these two results, the designed system shows a good linear relationship between the low concentration (0.02 - 0.5 PPM) of the water solution and the real part of the impedance. However, the relationship was changed from linear to logarithmic scale at the high concentration (0.05 - 10 PPM) of the water solution. The computational formula of concentration was formed from these results. This system has a potential to be used in-situ nitrate contamination detection with real-time monitoring.
A robust vanishing point estimation method for lane detection

Vanishing points are often used as constraints in lane detection or road following systems of intelligent vehicles. This paper proposes a new method for vanishing point estimation in consecutive frames based on computer vision. Parallel lines in the real world converge to vanishing points on an image plane, caused by the perspective projection. According to the duality between points and lines, estimation of vanishing points can be converted to a problem of line parameter estimation in a parameter space. Firstly, straight lines are detected from an extracted edge map of a road image by the Progressive Probability Hough Transform (PPHT) incorporated with gradient orientation constraints. Then, vanishing points are estimated via the Maximum A Posteriori (MAP) estimate, integrating information at the current frame and the vanishing point estimated at the previous frame into a probabilistic framework. For the detected lines are noisy, a weight is put on each line to indicate the probability ofbeing an inlier. But the weights are unknown, which are regarded as hidden variables here. Thus the Expectation Maximum (EM) algorithm is adopted to solve the MAP problem with hidden variables. Experimental results show the efficiency and robustness ofthe proposed method.
Accuracy and precision of linear measurements in cone beam computed tomography Accuitomo tomograms obtained with different reconstruction techniques.

OBJECTIVES To assess the accuracy and precision of linear measurements, the influence of different object positions in cone beam CT (CBCT) images and the effect of different systems for reformatting and viewing the tomograms on measurement values. METHODS An object consisting of Plexiglas plates with metal spheres was radiographically examined in three positions using the CBCT unit Accuitomo. Tomograms were reformatted using the i-Dixel software and Sectra picture archiving and communication system (PACS) multiplanar reformatting (MPR). Two observers measured 20 linear distances in axial, frontal and sagittal planes. Physical measurements of actual distances by means of a digital caliper served as the gold standard. RESULTS For measurements performed on the Accuitomo and Sectra PACS workstations, the mean differences between repeated measurements were below 0.13 mm (standard deviation (SD) 0.13 mm) and 0.21 mm (SD 0.18 mm), respectively. Mean differences between the two observers were below 0.11 mm (SD 0.07 mm) and 0.15 mm (SD 0.09 mm). The mean difference between the gold standard and the basic position when using the Accuitomo workstation, was -0.08 mm (SD 0.21 mm) and for a deviated/rotated position -0.08 mm (SD 0.23 mm) and -0.09 mm (SD 0.20 mm). None was statistically significant (P > 0.05). For measurement performed on MPR tomograms using the Sectra PACS workstation, mean differences were -0.09 mm (SD 0.17 mm) for basic position, and -0.08 mm (SD 0.19 mm) and -0.13 mm (SD 0.15 mm) for deviated and rotated positions, respectively. The mean difference between gold standard and basic/rotated positions was statistically significant, with P = 0.032 and P = 0.002. CONCLUSIONS Our study confirms previous findings indicating that measurements in 3DX Accuitomo FPD (flat panel detector) tomograms show a high level of agreement with actual distances. Our findings suggest the possibility of minor distortion in tomograms reformatted by means of Sectra PACS MPR.
Potent and selective peptide agonists of alpha-melanotropin action at human melanocortin receptor 4: their synthesis and biological evaluation in vitro.

alpha-Melanotropin (alphaMSH) and several of its derivatives are potent but not selective agonists at melanocortin receptors 3, 4, and 5 present in the brain (MC3-5R). To differentiate between the physiological role of hMC-4R (believed to be involved in regulation of energy balance) from those of melanocortin receptors 3 and 5, potent and receptor-specific agonists are needed. Therefore, the cyclic derivatives of alphaMSH of a general structure, cyclo(X-His-d-Phe-Arg-Trp-Y)-NH(2), where X is succinic acid or an omega-amino-carboxylic acid, and Y is an alpha,omega-di-amino-carboxylic acid or an omega-carboxy-alpha-amino acid, were prepared and tested in binding assays and in cAMP assays on CHO cells expressing hMC3-5R. Several of the 21-membered or larger lactams turned out to be potent and hMC-4R-selective agonists. For instance, cyclo(CO-CH(2)-CH(2)-CO-His-d-Phe-Arg-Trp-Dab)-NH(2) (Dab: 2,4-di-amino-butyric acid) was a potent agonist at hMC-4R (EC(50) = 4 nM) with 55-fold selectivity over hMC-3R and greater than 1000-fold selectivity over hMC-5R. Another potent and selective compound was cyclo(NH-CH(2)-CH(2)-CO-His-d-Phe-Arg-Trp-Glu)-NH(2): EC(50) about 1 nM at hMC-4R, with 90-fold selectivity over hMC-3R and greater than 2000-fold selectivity over hMC-5R.
Genetic Monitoring for Managers: A New Online Resource

Abstract Monitoring our natural resources will increasingly rely on genetic tools in order to understand and respond to invasive species, habitat degradation, fragmentation, disease, or climate-related changes. In recent years, the rapidly evolving field of genetic monitoring has seen explosive growth in sampling methods, genetic markers, and analytical approaches designed to estimate a wide range of parameters from connectivity to population growth rates. Some of these methods have taken root and now dominate particular aspects of population assessment and monitoring, whereas others have seen less success in real-world applications. To aid managers and researchers with limited genetics experience, we developed a web-based resource to help them identify which, if any, molecular genetic methods would be appropriate for population assessments or monitoring. The site was developed in cooperation with a team of experts in fields such as evolutionary biology, demographic parameter estimation, and exotic specie.
A global BMI algorithm based on the generalized benders decomposition

We present a new algorithm for the global solution of optimization problems involving bilinear matrix inequalities (BMIs). The method is based on a technique known in large-scale and global optimization as the generalized Benders decomposition. It extends the GOP algorithm of Visweswaran and Floudas for bilinear and biconvex programming to problems with BMI constraints.