Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of a Bacillus subtilis spoIIGA allele that suppresses processing-negative mutations in the Pro-sigma E gene (sigE)

sigma E, a sporulation-essential sigma factor of Bacillus subtilis, is formed by a developmentally regulated proteolysis which removes 27 to 29 amino acids from the amino terminus of an inactive precursor protein (Pro-sigma E). A mutation which facilitates the conversion of inefficiently processed Pro-sigma E variants into mature sigma E was identified and mapped to spoIIGA. The isolation of such a mutation argues that SpoIIGA is directly involved in the Pro-sigma E processing reaction.
Estimating consensus and associated uncertainty between inherently different species distribution models

Forecasting shifts in biome and species distribution is crucially needed in the current context of global change. So far, most projections of vegetation distribution rely on correlative species distribution models (SDMs). Yet, process‐based or hybrid models based on explicit physiological description may be more robust to extrapolation under future climatic conditions. Differences between model projections may be wide, leading to scepticism among environmental stakeholders. Here, we propose to combine outputs of several distribution models based on physiological responses, to produce both consensual maps of occurrences and maps of associated uncertainty. The consensus map relies on the conditional projections of each SDM. Because the models used are based on processes, their errors are likely to vary consistently with climate as some processes not implemented in a model might be important under a given set of climatic conditions. Uncertainty of the consensus model is thus assessed through multimodel regression of deviance maps with respect to current climatic conditions, and can be extrapolated to forecast climates. We illustrate this approach using three SDMs, on three widely distributed European trees (Fagus sylvatica L., Quercus robur L. and Pinus sylvestris L.), and project their distributions under two scenarios. The conditional consensus outperforms classical methods of model consensus (i.e. to use the mean, the median or a weighted average of individual SDM outputs) in projecting current occurrences. Consistently, with the results of individual SDMs, the conditional consensus projects that the suitable areas for F. sylvatica and Q. robur will expand towards north‐eastern Europe, while that of P. sylvestris will contract. Projections of future occurrence are most uncertain towards the margins of the distribution (particularly the trailing edge). Our approach can help modellers identify the limitations of each SDM and stakeholders pinpoint the regions of models agreement and highest certainty.
Circular Polarization in Turbulent Blazar Jets

Circular polarization (CP) provides an invaluable probe into the underlying plasma content of relativistic jets. CP can be generated within the jet through a physical process known as linear birefringence. This is a physical mechanism through which initially linearly polarized emission produced in one region of the jet is attenuated by Faraday rotation as it passes through other regions of the jet with distinct magnetic field orientations. Marscher developed the turbulent extreme multi-zone (TEMZ) model of blazar emission which mimics these types of magnetic geometries with collections of thousands of plasma cells passing through a standing conical shock. I have recently developed a radiative transfer algorithm to generate synthetic images of the time-dependent circularly polarized intensity emanating from the TEMZ model at different radio frequencies. In this study, we produce synthetic multi-epoch observations that highlight the temporal variability in the circular polarization produced by the TEMZ model. We also explore the effect that different plasma compositions within the jet have on the resultant levels of CP.
Identification of Chromera velia by fluorescence in situ hybridization.

Chromera velia is evolutionarily the closest free-living and photosynthetic organism to the medically important obligatory parasitic apicomplexans that cause diseases including malaria and toxoplasmosis. In this study, a novel oligonucleotide probe targeting C. velia's small subunit ribosomal RNA was designed. To enable usage of this probe as a detection tool, a fluorescence in situ hybridization (FISH) protocol was optimized. The results obtained showed that when used in combination, the C. velia CV1 probe and optimized FISH protocol enabled efficient detection of C. velia in culture. This new technique will allow a better understanding of the ecological role of C. velia within the coral microhabitat.
On the design of isotropic magnetic metamaterials

In this paper new 3D-isotropic magnetic resonators are proposed. These new particles possess spatial symmetries under whose all second order (pseudo-)tensors are reduced to (pseudo-)scalars. If then the contribution of higher order tensors is neglected, the particles are isotropic. To confirm that proposed particles still generate magnetic response, a quasi-static model, showing the qualitative behavior of the reported resonators, is proposed. Finally, the isotropy is experimentally checked by measuring the transmission coefficient through a waveguide loaded with such 3D particle in several orientations and results are compared with some previous proposals lacking these symmetries
Ligand‐Directed Profiling of Organelles with Internalizing Phage Libraries

Phage display is a resourceful tool to, in an unbiased manner, discover and characterize functional protein‐protein interactions, create vaccines, and engineer peptides, antibodies, and other proteins as targeted diagnostic and/or therapeutic agents. Recently, our group has developed a new class of internalizing phage (iPhage) for ligand‐directed targeting of organelles and to identify molecular pathways within live cells. This unique technology is suitable for applications ranging from fundamental cell biology to drug development. This unit describes the methods for generating and screening the iPhage display system, and explains how to select and validate candidate internalizing homing peptide. © 2015 by John Wiley & Sons, Inc.
Vincristine-induced self-association of calf brain tubulin.

The vincristine-induced self-association of tubulin has been examined in a sedimentation velocity study as a function of free drug concentration in PG buffer (0.01 M NaPi and 10(-4) M GTP, pH 7.0) at 20 degrees C. Analysis of the weight-average sedimentation coefficient (S20,w) as a function of protein concentration showed a good fit with the model of an indefinite, isodesmic self-association mechanism. Analysis of the apparent association constants in terms of the Wyman linkage relations showed a good fit to mediation of the self-association by the binding of one ligand molecule. The intrinsic association constant for dimerization of the vincristine-liganded tubulin was found to be 3.8 X 10(5) M-1, and the intrinsic equilibrium constant for the binding of the self-association-linked vincristine molecule had a value of 3.5 X 10(4) M-1, consistent with that measured by fluorescence in our laboratory [Prakash, V. , & Timasheff, S. N. (1983) J. Biol. Chem. 258, 1689-1697]. Both reactions are stronger in the presence of vincristine than of vinblastine, reflecting the oxidation of a -CH3 group to -CHO when going from the latter drug to the former one.
Solid Oxide Fuel Cell with DC-DC Converter System: Control and Grid Interfacing

Fuel cell unit generally has low voltage DC as output. To increase the output voltage, fuel cell stack is used where number of single unit fuel cell are connected in series or parallel. To step-up or step-down the output voltage of solid oxide fuel cell (SOFC), DC-DC converter is used. The DC output voltage of the converter is converted to AC with the help of DC-AC inverter. This paper develops MATLAB/Simulink model of fuel cell based power system (FCPS) comprising of fuel cell stack, DC-DC converter and DC-AC inverter. Sliding mode control (SMC) scheme is implemented in DC-DC buck converter, which guarantees stable output voltage despite transient variations in output voltage of fuel cell. Hysteresis current controller (HCC) scheme is implemented in DC-AC inverter which enables the fuel cell stack to supply utility AC voltage to grid and other power applications.
The Edinburgh Postnatal Depression Scale: validation on a Swedish community sample

The Edinburgh Postnatal Depression Scale (EPDS) was designed to be used by community health workers to screen for postnatal depression. We report data from a population‐based sample of 1655 women who completed the EPDS at 2 months and 3 months postpartum. A total of 128 women were interviewed with the Montgomery Asberg Depression Rating Scale (MADRS) and assessed according to DSM‐III‐R criteria for major depression. A cut‐off score of 11.5 on the EPDS identified all but two women with major depression, giving it a sensitivity of 96%, a specificity of 49% and a positive predictive value of 59%. This study supports the validity of the EPDS shown in earlier studies, and indicates that the scale is a useful screening instrument for identifying postnatal depression in primary health care in Sweden.
A Joint Model of Random Forest and Artificial Neural Network for the Diagnosis of Endometriosis

Endometriosis (EM), an estrogen-dependent inflammatory disease with unknown etiology, affects thousands of childbearing-age couples, and its early diagnosis is still very difficult. With the rapid development of sequencing technology in recent years, the accumulation of many sequencing data makes it possible to screen important diagnostic biomarkers from some EM-related genes. In this study, we utilized public datasets in the Gene Expression Omnibus (GEO) and Array-Express database and identified seven important differentially expressed genes (DEGs) (COMT, NAA16, CCDC22, EIF3E, AHI1, DMXL2, and CISD3) through the random forest classifier. Among these DEGs, AHI1, DMXL2, and CISD3 have never been reported to be associated with the pathogenesis of EMs. Our study indicated that these three genes might participate in the pathogenesis of EMs through oxidative stress, epithelial–mesenchymal transition (EMT) with the activation of the Notch signaling pathway, and mitochondrial homeostasis, respectively. Then, we put these seven DEGs into an artificial neural network to construct a novel diagnostic model for EMs and verified its diagnostic efficacy in two public datasets. Furthermore, these seven DEGs were included in 15 hub genes identified from the constructed protein–protein interaction (PPI) network, which confirmed the reliability of the diagnostic model. We hope the diagnostic model can provide novel sights into the understanding of the pathogenesis of EMs and contribute to the clinical diagnosis and treatment of EMs.
In vitro expression of receptor activator of nuclear factor-kappaB ligand and osteoprotegerin in cultured equine articular cells.

OBJECTIVE To determine concentrations of receptor activator of nuclear factor-kappaB ligand (RANKL) and osteoprotegerin (OPG) in equine chondrocytes and synoviocytes and to quantify changes in the OPG:RANKL ratio in response to exogenous factors. SAMPLE POPULATION Samples of articular cartilage and synovium with grossly normal appearance obtained from metacarpophalangeal and metatarsophalangeal joints of 5 adult (1- to 8-year-old) horses. PROCEDURES Cell cultures of chondrocytes and synoviocytes were incubated with human recombinant interleukin-1beta (hrIL-1beta; 10 ng/mL), lipopolysaccharide (LPS; 10 microg/mL), or dexamethasone (100nM) for 48 hours. Negative control cultures received no treatment. Cells and spent media were assayed for RANKL and OPG concentrations by use of western blot and immunocytochemical analyses. Spent media were also assayed for OPG concentration by use of an ELISA. RESULTS RANKL and OPG were expressed in equine chondrocytes and synoviocytes in vitro. Cell-associated RANKL and OPG concentrations were not impacted by exogenous factors. Soluble RANKL release into media was significantly increased by hrIL-1beta in chondrocyte but not in synoviocyte cultures. Soluble OPG release into media was significantly increased by hrIL-1beta and LPS in chondrocyte but not in synoviocyte cultures. The soluble OPG:RANKL ratio was significantly increased by LPS in chondrocyte cultures. Dexamethasone decreased OPG expression in synoviocytes. CONCLUSIONS AND CLINICAL RELEVANCE RANKL and OPG proteins were expressed in equine articular cells. Release of these proteins may affect osteoclastogenesis within adjacent subchondral bone. Thus, RANKL and OPG may have use as biomarkers and treatment targets in horses with joint disease.
Immunocytochemical Detection of Synaptophysin in Enteric Neurones during Prenatal Development in the Rat Stomach

In this study, the localization and appearance of synaptophysin‐immunoreactive (IR) nerve cells and their relationships with the developing gastric layers were studied by immunocytochemistry and light microscopy in the embryonic rat stomach. The stomachs of Wistar rat embryos aged 13–21 days were used. The first neuronal bodies and their processes containing synaptophysin‐immunoreactivity were observed on embryonic day 13. In contrast, synaptophysin‐IR nerve terminals were first observed between mesenchymal cells on embryonic day 14. These results indicate that synaptophysin is expressed in growing neurits and neuronal cell bodies before these neurones have established synaptic connections. The occurrences of mesenchymal cell condensation near synaptophysin‐IR neuroblasts on embryonic day 15 reflect an active nerve element‐specific mesenchymal cell induction resulting in the morphogenesis of muscle cells. Similarly, the appearance of glandular structures after synaptophysin‐IR neuroblasts, on embryonic day 18, suggests that the epithelial differentiation may be closely related to the neuronal maturation as well as other factors. Finally, synaptophysin is functionally important in neuronal development and maturation, together with the establishment of neuroneuronal and neuromuscular contacts and in epithelial differentiation.
The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis)

Abstract The silky shark mitogenome (GeneBank accession number KF801102) has a total length of 17,774 bp, the base composition of the genomes was as follows: A (31.36%), T (30.18%), C (25.27%) and G (13.17%), which demonstrated an A + T-rich feature (61.64%), similar to other elasmobranch mitogenomes. The mitochondrial genome contained 13 protein-coding genes and 23 tRNA genes. The tRNA genes ranged from 70 to 72 bp. The gene order was the same as in other vertebrates and teleosts.
Horizontal chromosome transfer and rational strategies to manage Fusarium vascular wilt diseases.

An adequate supply of healthy plants is essential to feed a growing population. Many plant pathogens are highly destructive, and consequently threaten global food security. The negative impact of plant pathogens on human society was illustrated by the Irish potato famine of the 1840s, the Bengal famine of the 1940s and the US Southern corn leaf blight epidemic of 1970–1971. These examples, recorded in history accounts and textbooks, may seem remote to us; however, the devastation caused by plant pathogens is not limited to the past. Today, plant pathogens continue to hamper agricultural production and threaten the wellbeing of human society. One such example is the recent spread of Panama disease of banana, caused by Fusarium oxysporum f. sp. cubense (Foc) tropic race 4 (TR4), from South-East Asia to Mozambique and Jordan (Butler, 2013). The first Panama disease outbreak caused by Foc race 1 almost destroyed the banana industry in the 1950s. The crisis was resolved by replacing the susceptible ‘Gros Michel’ cultivar with the race 1-resistant Cavendish cultivar (Ploetz, 2006). Unfortunately, the newly evolved TR4 is highly virulent to Cavendish. As bananas and plantains are significant staple foods and represent a primary dietary source of carbohydrates in Africa, South-East Asia and tropical America, the spread of Panama disease could potentially create localized food shortages, intensify world hunger and exacerbate poverty in developing nations. The causal agent of Panama disease, Foc, is one member of the root-infecting fungal pathogens in the F. oxysporum species complex (FOSC). Members within this species complex cause destructive and intractable Fusarium vascular wilts in over 100 plant species, ranging from gymnosperms to angiosperms and monocots to dicots. Listed as one of the top 10 fungal pathogens, diseases caused by F. oxysporum challenge the production of numerous economically important crops, including banana (Musa acuminata), cotton (Gossypium hirsutum), canola (Brassica napus) and tomato (Solanum lycopersicum) (Ma et al., 2013). As a species complex, F. oxysporum has a very broad host range. Interestingly, individual F. oxysporum isolates often exhibit a high degree of host specificity; a single pathogenic form usually infects a single plant species. Isolates with pathogenicity for the same host are grouped into the same forma specialis. For instance, isolates that are pathogenic to banana plants are classified as F. oxysporum f. sp. cubense (Foc) and those that infect tomato plants are classified as F. oxysporum f. sp. lycopersici (Fol).
Platelets, after Exposure to a High Shear Stress, Induce IL-10-Producing, Mature Dendritic Cells In Vitro1

There is evidence for immune system involvement in atherogenesis. In the present study the effect of platelets on dendritic cells (DC), an important immunologic regulator, was examined in vitro. Platelet-rich plasma, after exposure to shear stress, was added to human monocyte-derived immature DC, which were then examined for surface Ag expression, allogeneic T lymphocyte stimulatory activity, and cytokine production. After exposure, the number of anti-CD40 ligand (anti-CD40L) and anti-P-selectin IgG molecules bound per platelet was increased. These activated platelets induced DC maturation, as revealed by significant up-regulation of CD83, CD80, and CD86 Ags. The addition of platelets in the presence of IFN-γ plus LPS significantly enhanced IL-10 production from immature DC. After platelet addition, mature DC provoked a significant proliferation of allogeneic naive T lymphocytes. These activated T cells showed lower IFN-γ production than those stimulated by LPS- and IFN-γ-treated DC. CD40L on the platelet surface was not involved in maturation of DC, as mAb to CD40L failed to block maturation. The effect of platelets was observed even if platelets and DC were separated using large pore-sized membranes or when platelets were depleted from plasma by centrifugation. Furthermore, it was abrogated after the depletion of protein fraction. Thus, soluble protein factors excreted from activated platelets contribute to IL-10-producing DC maturation.
Performance Analysis of Multiple-Relay Decode-and-Forward Cooperation System

In this paper, we analyze the impact of the detection error at the relay node to the performance of the decode- and-forward cooperation system. We apply a simple detector, where no channel state information between the source node and the relay node is available at the destination, and maximum ratio combining is performed without considering whether the forwarded symbol from the relay is incorrect. With such an assumption, we analyze the error performance of the system with multiple relay nodes, and demonstrate the resulting error floor in this system. To compensate for the detection error at the relay node, we propose a relay selection protocol, which can lower the error floor and nearly achieve full diversity order.
Topographical distribution of muscarinic cholinergic receptors in the cerebellar cortex of the mouse, rat, guinea pig, and rabbit: A species comparison

Light microscopic autoradiography of [3H]quinuclidinyl benzilate (QNB) binding sites was used to study the distribution of muscarinic acetylcholine receptors in the mouse, rat, guinea pig, and rabbit cerebellar cortex. In the mouse, the laminar distribution of grain density was similar throughout the cortex, with slightly higher levels over lobules IX and X. The highest [3H]QNB labeling was present over the granule cell layer, and low levels were observed over the molecular layer. In the rat, the general distribution was similar to that of the mouse in that the granule cell layer was most densely labeled and the highest concentration of [3H]QNB binding sites was present in lobules IX and X of the archicerebellum. In these lobules, however, the laminar distribution of grain density was reversed so that the molecular layer was more densely labeled than the granule cell layer. In addition, several discrete columns of elevated grain density traversed the granule cell layer in caudal regions of lobule IX. The distribution of [3H]QNB binding sites in the guinea pig cerebellum was similar to that of the rat in that the molecular layer of lobules IX and X was again more intensely labeled than other cerebellar regions. In the remaining lobules, grain density was equal over the granule cell and molecular layers. In the rabbit cerebellar cortex, slightly higher grain density was observed in the granule cell layer than in the molecular layer. In lobules IX and X and in the hemisphere of X, the Purkinje cell layer was most densely labeled; parasagittal columns of very high grain density were present over the molecular layer of several cortical regions, including lobules I, II, III, IV, V, IX, X, and the hemispheres of IX and X.
Lidocaine-based Topical Anesthetic With Disinfectant (LidoDin) Versus EMLA for Venipuncture: A Randomized Controlled Trial

ObjectiveTo examine the efficacy and safety of a new topical anesthetic containing a disinfection ingredient (LidoDin cream) in reducing the pain associated with venipuncture by comparing it with the proven eutectic mixture of lidocaine 2.5% and prilocaine 2.5% (EMLA cream). MethodsA single-blind, randomized, controlled trial was conducted on a study population consisting of a convenience sample of patients aged 12 to 16 years who presented at our Emergency Department between November 2007 and April 2008. The Visual Analog Scale (VAS) was used for pain assessment. Before the study, the bactericidal effect of the LidoDin cream on skin flora was tested. ResultsTwenty patients were enrolled to each arm of the study. Mean patient age was 13.6 years for the LidoDin group and 14.12 years for the EMLA group (P=0.347). Male patients accounted for 55% of the patients in the LidoDin group, compared with 40% in the EMLA group (P=0.527). Skin reaction scores of the LidoDin group for erythema and edema were not statistically different than those of the EMLA group (P=0.73 and P=0.75, respectively). Patient VAS scores and nurse VAS scores of the LidoDin group were not statistically different than those of the EMLA group (P=0.57 and P=0.93, respectively). DiscussionThis pilot study demonstrated that LidoDin and EMLA seem to be equally safe and effective topical anesthetics for venipuncture. Future studies are planned to determine, if LidoDin reduces the rate of local skin infection in patients treated with multiple daily subcutaneous injections of medications.
Cloning and characterization of tetM gene from a Ureaplasma urealyticum strain

We have cloned a 4.9-kilobase (kb) HincII fragment which contains a tetracycline resistance determinant (tetM) from the chromosome of Ureaplasma urealyticum. The 4.9-kb HincII fragment contains DNA in addition to the structural gene, is closely related to the previously characterized 5.0-kb fragment from pJI3, and contains no normal ureaplasmal DNA sequences.