Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region

In order to develop a diagnostic tool to identify phytoplasmas and classify them according to their phylogenetic group, we took advantage of the sequence diversity of the 16S-23S intergenic spacer regions (SRs) of phytoplasmas. Ten PCR primers were developed from the SR sequences and were shown to amplify in a group-specific fashion. For some groups of phytoplasmas, such as elm yellows, ash yellows, and pear decline, the SR primer was paired with a specific primer from within the 16S rRNA gene. Each of these primer pairs was specific for a specific phytoplasma group, and they did not produce PCR products of the correct size from any other phytoplasma group. One primer was designed to anneal within the conserved tRNA(Ile) and, when paired with a universal primer, amplified all phytoplasmas tested. None of the primers produced PCR amplification products of the correct size from healthy plant DNA. These primers can serve as effective tools for identifying particular phytoplasmas in field samples.
The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity

PpiD is a periplasmic folding helper protein of Escherichia coli. It consists of an N‐terminal helix that anchors PpiD in the inner membrane near the SecYEG translocon, followed by three periplasmic domains. The second domain (residues 264–357) shows homology to parvulin‐like prolyl isomerases. This domain is a well folded, stable protein and follows a simple two‐state folding mechanism. In its solution structure, as determined by NMR spectroscopy, it resembles most closely the first parvulin domain of the SurA protein, which resides in the periplasm of E. coli as well. A previously reported prolyl isomerase activity of PpiD could not be reproduced when using improved protease‐free peptide assays or assays with refolding proteins as substrates. The parvulin domain of PpiD interacts, however, with a proline‐containing tetrapeptide, and the binding site, as identified by NMR resonance shift analysis, colocalized with the catalytic sites of other parvulins. In its structure, the parvulin domain of PpiD resembles most closely the inactive first parvulin domain of SurA, which is part of the chaperone unit of this protein and presumably involved in substrate recognition.
Three-dimensional facial analyses of Indian and Malaysian women

Context: Facial measurements serve as a valuable tool in the treatment planning of maxillofacial rehabilitation, orthodontic treatment, and orthognathic surgeries. The esthetic guidelines of face are still based on neoclassical canons, which were used in the ancient art. These canons are considered to be highly subjective, and there is ample evidence in the literature, which raises such questions as whether or not these canons can be applied for the modern population. Aims: This study was carried out to analyze the facial features of Indian and Malaysian women by using three-dimensional (3D) scanner and thus determine the prevalence of neoclassical facial esthetic canons in both the groups. Subjects and Methods: The study was carried out on 60 women in the age range of 18-25 years, out of whom 30 were Indian and 30 Malaysian. As many as 16 facial measurements were taken by using a noncontact 3D scanner. Statistical Analysis Used: Unpaired t-test was used for comparison of facial measurements between Indian and Malaysian females. Two-tailed Fisher exact test was used to determine the prevalence of neoclassical canons. Results: Orbital Canon was prevalent in 80% of Malaysian women; the same was found only in 16% of Indian women (P = 0.00013). About 43% of Malaysian women exhibited orbitonasal canon (P = 0.0470) whereas nasoaural canon was prevalent in 73% of Malaysian and 33% of Indian women (P = 0.0068). Conclusions: Orbital, orbitonasal, and nasoaural canon were more prevalent in Malaysian women. Facial profile canon, nasooral, and nasofacial canons were not seen in either group. Though some canons provide guidelines in esthetic analyses of face, complete reliance on these canons is not justifiable.
How do astrocytes shape synaptic transmission? Insights from electrophysiology

A major breakthrough in neuroscience has been the realization in the last decades that the dogmatic view of astroglial cells as being merely fostering and buffering elements of the nervous system is simplistic. A wealth of investigations now shows that astrocytes actually participate in the control of synaptic transmission in an active manner. This was first hinted by the intimate contacts glial processes make with neurons, particularly at the synaptic level, and evidenced using electrophysiological and calcium imaging techniques. Calcium imaging has provided critical evidence demonstrating that astrocytic regulation of synaptic efficacy is not a passive phenomenon. However, given that cellular activation is not only represented by calcium signaling, it is also crucial to assess concomitant mechanisms. We and others have used electrophysiological techniques to simultaneously record neuronal and astrocytic activity, thus enabling the study of multiple ionic currents and in depth investigation of neuro-glial dialogues. In the current review, we focus on the input such approach has provided in the understanding of astrocyte-neuron interactions underlying control of synaptic efficacy.
Decrease in Cell Viability Due to the Accumulation of Spermidine in Spermidine Acetyltransferase-deficient Mutant of Escherichia coli(*)

Physiological functions of spermidine acetyltransferase in Escherichia coli have been studied using the spermidine acetyltransferase (speG) gene-deficient mutant CAG2242 and the cloned speG gene. The growth of E. coli CAG2242 in the defined M9 medium was normal in the presence and absence of 0.5 mM spermidine. However, cell viability of E. coli CAG2242 at 48 h after the onset of growth decreased greatly by the addition of 0.5 mM spermidine. The amount of spermidine accumulated in the cells was approximately 3-fold that in the cells grown in the absence of spermidine. Transformation of the cloned speG gene to E. coli CAG2242 recovered the cell viability. Decrease in cell viability of E. coli CAG2242 was observed even when 0.5 mM spermidine was added at 24 h after the onset of growth. The results indicate that accumulated spermidine functions at the late stationary phase of growth. The accumulation of spermidine caused a decrease in protein synthesis but not in DNA and RNA synthesis at 28 h after the onset of growth. The synthesis of several kinds of proteins was particularly inhibited. They included ribosome modulation factor and OmpC protein. Since the ribosome modulation factor is essential for cell viability at the stationary phase of growth (Yamagishi, M., Matsushima, H., Wada, A., Sakagami, M., Fujita, N., and Ishihama, A.(1993) EMBO J. 12, 625-630), the decrease in the protein was thought to be one of the reasons for the decrease in cell viability. The decrease in the ribosome modulation factor mainly occurred at the translational level.
Glial‐ and fat‐specific expression of the rat glycerol phosphate dehydrogenase‐luciferase fusion gene in transgenic mice

Glycerol phosphate dehydrogenase (GPDH) is a metabolic enzyme that catalyzes the conversion of dihydroxyacetone phosphate to glycerol‐3‐phosphate. It provides phospholipid precursors for lipid biosynthesis and energy metabolism. In the brain, GPDH enzymatic activity, protein, mRNA are exclusively associated with oligodendroglial and Bergmann glial cells. Expression of GPDH in the brain increases dramatically during the active period of myelination, and is regulated by extracellular signals. In an effort to understand the mechanism that confers glial‐specific expression of GPDH, we have examined the role of the 5′ flanking sequence of the rat GPDH gene in conferring cell‐specific expression of reporter gene in transgenic mice. Luciferase reporter constructs containing either the full‐length GPDH 5′ flanking region (p4.3), or a distally truncated version (p2.6), were injected into mouse zygotes. Three independent lines of transgenic mice containing the p4.3, and seven lines of mice containing the p2.6 constructs, were analyzed. Luciferase enzyme activity was detectable only in brain and fat, not in other GPDH‐positive organs such as liver, muscle, and kidney. Both the full‐length and the distally deleted transgenes were expressed similarly in these two organs, indicating that the distal portion of the 5′ flanking region was not required for brain‐ and fat‐specific expression. Immunocytochemical analyses revealed that luciferase immunoreactivity colocalized with glial fibrillary acidic protein (GFAP)‐positive Bergmann glia in the cerebellum, and myelin basic protein (MBP)‐positive oligodendroglia in the cerebral cortex and the brainstem. Results here suggest that the rat GPDH 5′ flanking region directs glial‐specific expression of GPDH transcription in the brain, and provide a good model for analyses of changes in glial metabolism in response to extracellular perturbations in vivo. J. Neurosci. Res. 50:300–311, 1997. © 1997 Wiley‐Liss, Inc.
AtAIRP2 E3 Ligase Affects ABA and High-Salinity Responses by Stimulating Its ATP1/SDIRIP1 Substrate Turnover1

AtAIRP2 and SDIR1 RING E3 Ub ligases play combinatory roles in response to ABA and high-salinity stress during germination growth via the UPS-dependent down-regulation of ATP1/SDIRIP1 in Arabidopsis. AtAIRP2 is a cytosolic RING-type E3 ubiquitin ligase that positively regulates an abscisic acid (ABA) response in Arabidopsis (Arabidopsis thaliana). Yeast two-hybrid screening using AtAIRP2 as bait identified ATP1 (AtAIRP2 Target Protein1) as a substrate of AtAIRP2. ATP1 was found to be identical to SDIRIP1, which was reported recently to be a negative factor in ABA signaling and a target protein of the RING E3 ligase SDIR1. Accordingly, ATP1 was renamed ATP1/SDIRIP1. A specific interaction between AtAIRP2 and ATP1/SDIRIP1 and ubiquitination of ATP1/SDIRIP1 by AtAIRP2 were demonstrated in vitro and in planta. The turnover of ATP1/SDIRIP1 was regulated by AtAIRP2 in cell-free degradation and protoplast cotransfection assays. The ABA-mediated germination assay of 35S:ATP1/SDIRIP1-RNAi/atairp2 double mutant progeny revealed that ATP1/SDIRIP1 acts downstream of AtAIRP2. AtAIRP2 and SDIR1 reciprocally complemented the ABA- and salt-insensitive germination phenotypes of sdir1 and atairp2 mutants, respectively, indicating their combinatory roles in seed germination. Subcellular localization and bimolecular fluorescence complementation experiments in the presence of MG132, a 26S proteasome inhibitor, showed that AtAIRP2 and ATP1/SDIRIP1 were colocalized to the cytosolic spherical body, which lies in close proximity to the nucleus, in tobacco (Nicotiana benthamiana) leaf cells. The 26S proteasome subunits RPN12a and RPT1 and the molecular chaperones HSP70 and HSP101 were colocalized to these discrete punctae-like structures. These results raised the possibility that AtAIRP2 and ATP1/SDIRIP1 interact in the cytosolic spherical compartment. Collectively, our data suggest that the down-regulation of ATP1/SDIRIP1 by AtAIRP2 and SDIR1 RING E3 ubiquitin ligases is critical for ABA and high-salinity responses during germination in Arabidopsis.
Gene Expression Studies Demonstrate that the K-ras/Erk MAP Kinase Signal Transduction Pathway and Other Novel Pathways Contribute to the Pathogenesis of Cumene-induced Lung Tumors

National Toxicology Program (NTP) inhalation studies demonstrated that cumene significantly increased the incidence of alveolar/bronchiolar adenomas and carcinomas in B6C3F1 mice. Cumene or isopropylbenzene is a component of crude oil used primarily in the production of phenol and acetone. The authors performed global gene expression analysis to distinguish patterns of gene regulation between cumene-induced tumors and normal lung tissue and to look for patterns based on the presence or absence of K-ras and p53 mutations in the tumors. Principal component analysis segregated the carcinomas into groups with and without K-ras mutations, but failed to separate the tumors based on p53 mutation status. Expression of genes associated with the Erk MAP kinase signaling pathway was significantly altered in carcinomas with K-ras mutations compared to tumors without K-ras mutations or normal lung. Gene expression analysis also suggested that cumene-induced carcinomas with K-ras mutations have greater malignant potential than those without mutations. In addition, significance analysis of function and expression (SAFE) demonstrated expression changes of genes regulated by histone modification in carcinomas with K-ras mutations. The gene expression analysis suggested the formation of alveolar/bronchiolar carcinomas in cumene-exposed mice typically involves mutation of K-ras, which results in increased Erk MAP kinase signaling and modification of histones.
A Novel Spectral Index for Automatic Shadow Detection in Urban Mapping Based On WorldView-2 Satellite Imagery

In remote sensing, shadow causes problems in many applications such as change detection and classification. It is caused by objects which are elevated, thus can directly affect the accuracy of information. For these reasons, it is very important to detect shadows particularly in urban high spatial resolution imagery which created a significant problem. This paper focuses on automatic shadow detection based on a new spectral index for multispectral imagery known as Shadow Detection Index (SDI). The new spectral index was tested on different areas of WorldView-2 images and the results demonstrated that the new spectral index has a massive potential to extract shadows with accuracy of 94% effectively and automatically. Furthermore, the new shadow detection index improved road extraction from 82% to 93%.
The Network Structure of Organizational Vocabularies

Abstract We study organizational vocabularies as complex social structures emerging from the association between organizational participants and words they use to describe and make sense of their experiences at work. Using data that we have collected on the association between managers in a multi-unit international company and words they use to describe their organizational units and the overall company, we examine the relational micro-mechanisms underlying the observed network structure of organizational vocabularies. We find that members of the same subsidiary tend to become more similar in terms of the words they use to describe their units. Members of the same subsidiary, however, do not use the same words to describe the corporate group. Consequently, the structure of organizational vocabularies tends to support consistent local interpretations, but reveals the presence of divergent meanings that organizational participants associate with the superordinate corporate group.
Hepatitis Delta Antigen Mediates the Nuclear Import of Hepatitis Delta Virus RNA

ABSTRACT Hepatitis delta virus (HDV) RNA replicates in the nuclei of virus-infected cells. The mechanism of nuclear import of HDV RNA is so far unknown. Using a fluorescein-labeled HDV RNA introduced into partially permeabilized HeLa cells, we found that HDV RNA accumulated only in the cytoplasm. However, in the presence of hepatitis delta antigen (HDAg), which is the only protein encoded by HDV RNA, the HDV RNA was translocated into the nucleus, suggesting that nuclear import of HDV RNA is mediated by HDAg. Deletion of the nuclear localization signal (NLS) or RNA-binding motifs of HDAg resulted in the failure of nuclear import of HDV RNA, indicating that both the NLS and an RNA-binding motif of HDAg are required for the RNA-transporting activity of HDAg. Surprisingly, any one of the three previously identified RNA-binding motifs was sufficient to confer the RNA-transporting activity. We have further shown that HDAg, via its NLS, interacts with karyopherin α2 in vitro, suggesting that nuclear import of the HDAg-HDV RNA complex is mediated by the karyopherin α2β heterodimer. The nuclear import of HDV RNA may be the first biological function of HDAg in the HDV life cycle.
Association of Father Involvement and Neighborhood Quality with Kindergartners' Physical Activity: A Multilevel Structural Equation Model

Purpose. Examine the effects of father-child involvement and neighborhood characteristics with young children's physical activity (PA) within a multilevel framework. Design. Cross-sectional analysis of the Early Childhood Longitudinal Study—Kindergarten Cohort 1998. Setting. Nationally representative sample. Subjects. Data were available for 10,694 kindergartners (5–6 years; 5240 girls) living in 1053 neighborhoods. Measures. Parental report of child's PA level, father characteristics (e.g., time spent with child, age, education, socioeconomic status, hours worked), family time spent doing sports/activities together, and neighborhood quality (e.g., safety, presence of crime violence, garbage). Child weight status, motor skills, ethnicity, and television viewing were used as covariates. Analysis. Multilevel structural equation modeling with children nested within neighborhoods. Results. At the child level father-child time and family time doing sports together were positively associated with children's PA. At the neighborhood level parental perception of a neighborhood's safety for children to play outside fully mediated the effect of neighborhood quality on children's PA. Overall 19.1% and 7.6% of the variance in PA was explained at the child and neighborhood levels, respectively. Conclusions. Family-based interventions for PA should consider father-child time, with this contributing to a child's overall PA level. Further, neighborhood quality is an important predictor of PA only to the extent by which parents perceive it to be unsafe for their child to play outdoors.
BoobyTrap: On autonomously detecting and characterizing crawlers in P2P botnets

The ever-growing number of cyber attacks from botnets has made them one of the biggest threats on the Internet. Thus, it is crucial to study and analyze botnets, to take them down. For this, an extensive monitoring is a pre-requisite for preparing a botnet takedown, e.g., via a sinkholing attack. However, every new monitoring mechanism developed for botnets is usually tackled by the botmasters by introducing novel antimonitoring countermeasures. In this paper, we anticipate these countermeasures by proposing a set of lightweight techniques for detecting the presence of crawlers in P2P botnets, called BoobyTrap. For that, we exploit botnet-specific protocol and design constraints. We evaluate the performance of our BoobyTrap mechanism on two real-world botnets: Sality and ZeroAccess. Our results indicate that we can distinguish many crawlers from benign bots. In fact, we discovered close to 10 crawler nodes within our observation period in the Sality botnet and around 120 in the ZeroAccess botnet. In addition, we also describe the observable characteristics of the detected crawlers and suggest crawler improvements for enabling monitoring in the presence of the BoobyTrap mechanism.
InGaZnO Thin-Film Transistors With Coplanar Control Gates for Single-Device Logic Applications

Neuron thin-film transistors (TFTs) with coplanar control gates based on RF sputtering-deposited amorphous indium-gallium-zinc oxide (IGZO) layer are fabricated. Two coplanar control gates, capacitively coupled with the floating gate, can effectively control the neutron TFT. The drain current of the TFT can be controlled by the logic states (and the voltage magnitude) of the control gates, which is attributed to the modulation of an electron accumulation region in the IGZO channel layer. The neuron TFT can produce three output states, which could be used to implement an abacuslike counting scheme. It can also be used to implement the OR and AND logic functions on the same device.
Evaluation of thrombolysis in a porcine model of chronic deep venous thrombosis: an endovascular model.

PURPOSE The advancement of catheter-based interventions for vascular recanalization has underscored the need for an experimental animal model of vascular thrombosis that can be used for the evaluation of interventional therapies. In this model, a porcine model of deep venous thrombosis with a novel endovascular technique was described, and the efficacy of thrombolytic therapy with urokinase was evaluated. METHODS An endovascular device that consisted of a tapered polytetrafluoroethylene graft attached within a self-expanding nitinol stent was delivered to bilateral common iliac veins in 20 pigs. Venous thrombosis occurred as a result of flow stasis created by the intrastent stenosis. Catheter-directed pulse-spray thrombolysis with urokinase (250,000 units) and heparin (5000 IU) was performed on one limb while the contralateral limb received control saline solution. Thrombolysis was performed in 1 hour (n = 4), 8 hours (n = 4), 3 days (n = 4), 7 days (n = 4), and 14 days (n = 4) after the stent-graft deployment. Venography and intravascular ultrasound were used to evaluate the efficacy of thrombolysis. Light microscopy was used for histologic analysis of the thrombus. RESULTS Complete thrombolysis was achieved in groups with deep vein thrombosis that were younger than 1 day. Angioplasty of the tapered stent-grafts in the completely thrombolysed iliac vein was successful in restoring venous flow. The efficacy of thrombolysis in 3-day, 7-day, and 14-day groups was 86% +/- 7%, 73% +/- 13%, and 42% +/- 23%, respectively. The thrombolytic efficacy was enhanced to 92% +/- 16% and 86% +/- 18% (P <.05) in 3-day and 7-day groups, respectively, when doses of the pulse-spray thrombolysis were doubled. Increased dosages of the thrombolytic agent, however, did not significantly enhance the thrombus dissolution in the 14-day group. CONCLUSION The thrombolytic efficacy of urokinase correlated with the chronicity of deep venous thrombosis in our model. An increased dose of urokinase may be used to enhance the efficacy of thrombolysis in a 1-week-old thrombus.
MafB interacts with Gcm2 and regulates parathyroid hormone expression and parathyroid development

Serum calcium and phosphate homeostasis is critically regulated by parathyroid hormone (PTH) secreted by the parathyroid glands. Parathyroid glands develop from the bilateral parathyroid‐thymus common primordia. In mice, the expression of transcription factor Glial cell missing 2 (Gcm2) begins in the dorsal/anterior part of the primordium on embryonic day 9.5 (E9.5), specifying the parathyroid domain. The parathyroid primordium then separates from the thymus primordium and migrates to its adult location beside the thyroid gland by E15.5. Genetic ablation of gcm2 results in parathyroid agenesis in mice, indicating that Gcm2 is essential for early parathyroid organogenesis. However, the regulation of parathyroid development at later stages is not well understood. Here we show that transcriptional activator v‐maf musculoaponeurotic fibrosarcoma oncogene homologue B (MafB) is developmentally expressed in parathyroid cells after E11.5. MafB expression was lost in the parathyroid primordium of gcm2 null mice. The parathyroid glands of mafB+/− mice were mislocalized between the thymus and thyroid. In mafB−/− mice, the parathyroid did not separate from the thymus. Furthermore, in mafB−/− mice, PTH expression and secretion were impaired; expression levels of renal cyp27b1, one of the target genes of PTH, was decreased; and bone mineralization was reduced. We also demonstrate that although Gcm2 alone does not stimulate the PTH gene promoter, it associates with MafB to synergistically activate PTH expression. Taken together, our results suggest that MafB regulates later steps of parathyroid development, that is, separation from the thymus and migration toward the thyroid. MafB also regulates the expression of PTH in cooperation with Gcm2. © 2011 American Society for Bone and Mineral Research