Miracle-dz/UniFAR-FTUs huggingface dataset:
Shigella Spa33 Is an Essential C-ring Component of Type III Secretion Machinery*

Type III secretion machinery (TTSM), composed of a needle, a basal body, and a C-ring compartment, delivers a subset of effectors into host cells. Here, we show that Shigella Spa33 is an essential component of the C-ring compartment involved in mediating the transit of various TTSM-associated translocated proteins. Electron microscopic analysis and pull-down assay revealed Spa33 to be localized beneath the TTSM via interaction with MxiG and MxiJ (basal body components). Spa33 is also capable of interacting with Spa47 (TTSM ATPase), MxiK, MxiN (required for the transit of MxiH, the needle component), Spa32 (required for determining needle length), and several effectors. Genetic and functional analyses of the Spa33 C-terminal region, which is highly conserved in the SpaO-YscQ-HrcQB-FliN family, indicate that some of the conserved residues are crucial for needle formation via interactions with MxiN. Thus, Spa33 plays a central role as the C-ring component in recruiting/exporting TTSM-associated proteins.
Variability in CitXET expression and XET activity in Citrus cultivar Huangguogan seedlings with differed degrees of etiolation

Considering the known effects of xyloglucan endotransglycosylase (XET) on plant growth and development, we aimed to determine whether XETs help to regulate the growth and elongation of Huangguogan shoots and roots. We confirmed a possible role for XET during seedling etiolation. Our results revealed that the roots of etiolated seedlings (H-E) were longer than those of green seedlings (H-G). However, shoot length exhibited the opposite pattern. We also observed positive and negative effects on the xyloglucan-degrading activity of XET in the root sub-apical region and shoots of etiolated Huangguogan seedling, respectively. There was a significant down-regulation in CitXET expression in the etiolated shoots at 15 days after seed germination. On the contrary, it was significantly increased in the root sub-apical region of etiolated and multicolored seedlings at 15 days after seed germination. The XET coding sequence (i.e., CitXET) was cloned from Huangguogan seedlings using gene-specific primers. The encoded amino acid sequence was predicted by using bioinformatics-based methods. The 990-bp CitXET gene was highly homologous to other XET genes. The CitXET protein was predicted to contain 319 amino acids, with a molecular mass of 37.45 kDa and an isoelectric point of 9.05. The predicted molecular formula was C1724H2548N448O466S14, and the resulting protein included only one transmembrane structure. The CitXET secondary structure consisted of four main structures (i.e., 21% α-helix, 30.72% extended strand, 9.09% β-turn, and 39.18% random coil). Analyses involving the NCBI Conserved Domains Database (NCBI-CDD), InterPro, and ScanProsite revealed that CitXET was a member of the glycosyl hydrolase family 16 (GH16), and included the DEIDFEFLG motif. Our results indicate that the differed degrees of etiolation influenced the CitXET expression pattern and XET activity in Huangguogan seedlings. The differential changes in XET activity and CitXET expression levels in Huangguogan seedlings may influence the regulation of root and shoot development, and may be important for seedling etiolation.
Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation

Significance Significant progress has been achieved in our understanding of plant adaptive responses to ensure growth and reproduction in soils with low phosphate (Pi) availability. However, the potential role of epigenetic mechanisms in the modulation of these responses remains largely unknown. In this article, we describe dynamic changes in global DNA methylation patterns that occur in Arabidopsis plants exposed to low Pi availability; these changes are associated with the onset of Pi starvation responses. We show that the expression of a subset of low Pi-responsive genes is modulated by methylation changes and that DNA methylation is required for the proper establishment of developmental and molecular responses to Pi starvation. Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation–responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.
Effects of cleavage by a disintegrin and metalloproteinase with thrombospondin motifs-4 on gene expression and protein content of versican and aggrecan in the digital laminae of horses with starch gruel-induced laminitis.

OBJECTIVE To determine whether increased gene expression of a disintegrin and metalloproteinase with thrombospondin motifs-4 (ADAMTS-4) in laminae of horses with starch gruel-induced laminitis was accompanied by increased enzyme activity and substrate degradation. SAMPLE Laminae from the forelimb hooves of 8 healthy horses and 17 horses with starch gruel-induced laminitis (6 at onset of fever, 6 at onset of Obel grade 1 lameness, and 5 at onset of Obel grade 3 lameness). PROCEDURES Gene expression was determined by use of cDNA and real-time quantitative PCR assay. Protein expression and processing were determined via SDS-PAGE and quantitative western blotting. Protein distribution and abundance were determined via quantitative immunofluorescent staining. RESULTS ADAMTS-4 gene expression was increased and that of versican decreased in laminitic laminae, compared with expression in healthy laminae. Catalytically active ADAMTS-4 also was increased in the tissue, as were ADAMTS-4-cleavage fragments of versican. Immunofluorescent analyses indicated that versican was depleted from the basal epithelia of laminae of horses at onset of Obel grade 3 lameness, compared with results for healthy laminae, and this was accompanied by regional separation of basal epithelial cells from the basement membrane. Aggrecan gene and protein expression were not significantly affected. CONCLUSIONS AND CLINICAL RELEVANCE Changes in gene and protein expression of ADAMTS-4 and versican in the basal epithelium of laminitic laminae indicated a fundamental change in the physiology of basal epithelial cells. This was accompanied by and may have caused detachment of these cells from the basement membrane.
Osteolytic Indicators Found in Total Knee Arthroplasty Synovial Fluid Aspirates

Interleukin-1β and tartrate resistant acid phosphatase concentrations in synovial fluid aspirates were examined to determine if they could be used as indicators of increased synovial inflammation and an osteolytic reaction in patients having total knee arthroplasty. Synovial aspirates were obtained from seven patients with severely osteoarthritic knees that were scheduled for primary total knee arthroplasty and from 20 patients with knees scheduled for total knee arthroplasty revision. Eleven of the revision cases involved titanium alloy prostheses and nine involved cobalt chrome alloy prostheses. The interleukin-1β and tartrate resistant acid phosphatase concentrations were obtained and compared between the group having primary total knee arthroplasty and the group having revision total knee arthroplasty. The knees having revision surgery had higher concentrations of interleukin-1β and tartrate resistant acid phosphatase than did the knees having primary total knee arthroplasty. These results indicate a greater inflammatory and osteolytic response in knees having revision surgery. Although the osteoarthritic knees and the knees needing revision surgery in this study are considered to have an inflammatory state, it was only after total knee arthroplasty when particulate wear debris would be present that appreciable concentrations of interleukin-1β and tartrate resistant acid phosphatase were produced.
From Domination to a Caring Ecology: Healing Paradigms and Creative Practices for the Apprenticene

This article explores, in four main sections, the idea of designing and applying human-environment paradigms. First, Caring Ecology criteria for human-environment paradigms are proposed that combine the principles of caring in Partnership Studies, with compatible ecological conceptions of humans’ dependent and integrated relationship within Earth systems. Next, these criteria are used to evaluate the strengths and weaknesses of five environmental paradigms which sets the stage for the following section critiquing the current “Anthropocene” paradigm and proposing a counter-paradigm: the “Apprenticene. ” Paradigms suggest roles and actions and “Apprenticene Practices” are proposed, calling for humans to see our dependence on Earth systems, heal our story as we accept past failures, and learn by apprenticing ourselves to the Earth system. Finally, these Apprenticene Practices are illustrated in an example of a creative practice called Earth Systems Journey that engages youth with an integrated experience of their human-natural environment. The paper concludes with reflections on how Partnership Studies and ecological principles can work together to support a thriving future for humans and the rest of nature.
A conserved motif in transmembrane helix 1 of diphtheria toxin mediates catalytic domain delivery to the cytosol

A 10-aa motif in transmembrane helix 1 of diphtheria toxin that is conserved in anthrax edema factor, anthrax lethal factor, and botulinum neurotoxin serotypes A, C, and D was identified by blast, clustal w, and meme computational analysis. Using the diphtheria toxin-related fusion protein toxin DAB389IL-2, we demonstrate that introduction of the L221E mutation into a highly conserved residue within this motif results in a nontoxic catalytic domain translocation deficient phenotype. To further probe the function of this motif in the process by which the catalytic domain is delivered from the lumen of early endosomes to the cytosol, we constructed a gene encoding a portion of diphtheria toxin transmembrane helix 1, T1, which carries the motif and is expressed from a CMV promoter. We then isolated stable transfectants of Hut102/6TG cells that express the T1 peptide, Hut102/6TG-T1. In contrast to the parental cell line, Hut102/6TG-T1 cells are ca. 104-fold more resistant to the fusion protein toxin. This resistance is completely reversed by coexpression of small interfering RNA directed against the gene encoding the T1 peptide in Hut102/6TG-T1 cells. We further demonstrate by GST-DT140-271 pull-down experiments in the presence and absence of synthetic T1 peptides the specific binding of coatomer protein complex subunit β to this region of the diphtheria toxin transmembrane domain.
Intramuscular Transplantation of Myogenic Cells in Primates: Importance of Needle Size, Cell Number, and Injection Volume

The aim of this study was to quantitatively define the main measurable technical parameters for the intramuscular transplantation of myogenic cells in primates. Myoblasts transduced with the gene coding for β-galactosidase were injected into the skeletal muscles of 15 monkeys. The following parameters were studied: needle size, number of cells per injection, and volume of cell suspension per injection. Monkeys were immunosuppressed with tacrolimus. The cell-injected sites were biopsied 1 or 2 months later. Biopsies were examined histo logically to assess the myoblast engraftment and the muscle structure. The conclusions were as follows: (1) Needles should be thin enough to avoid important tissue damage and allow muscle regeneration as satisfactory as possible. Among those tested, 27G should be the choice if the length is consistent with depth of injection. (2) At least 100,000 cells should be delivered per centimeter of needle trajectory. (3) The smallest volumes of cell suspension per injection should be used. In this study, 1 μl/cm of injection trajectory was sufficient. In principle, these parameters apply to muscles in which no damage occurred other than the injections.
Incomplete contracts, control rights and integration decisions in economic organisations.

This thesis comprises an introduction and four distinct chapters. Its central theme is the role played by the allocation of asset ownership rights in motivating asset-specific investment, when contracts are incomplete. Chapter 1 considers the debt financing of an entrepreneurial project. To encourage asset-specific investment and loan repayment, debt structure should minimise both (voluntary) strategic default and liquidation following (unavoidable) liquidity default. Liquidation incentives are critical and shown to depend crucially on creditor characteristics. In general, borrowing from multiple creditors with contrasting attributes is found optimal. The benefits of borrowing from a creditor also undertaking project trade are explored. In Chapter 2 the relationship between asset ownership and investment specificity is examined. Asset control encourages efficient, asset-specific investment by owners. However, lock-in fears lead non-owners to choose widely applicable but less effective investment. The interactions between asset ownership, firms' technology choices and workers' investments are considered. In particular, it is found that the costs and benefits of individual integration decisions are sensitive to overall industry structure. The specificity framework is extended in Chapter 3 to model a retailer's product choice. Vertical merger encourages investment in integrated supply and foreclosure of non-integrated manufacturers. An anti-competitive as opposed to an efficiency interpretation depends delicately on the trade-off between the benefits of supplier-specific investment and multi-product retailing. Where retailers compete, it is shown that vertical integration implements effective competition-reducing differentiation strategies. In Chapter 4 vertical integration, through the incentive effects of asset ownership, is shown to amount to a specialisation decision. The attractions of encouraging investment in input as opposed to final good production depend on the effectiveness of investment at each manufacturing stage, and the scale benefits of input sales to generally rivalrous downstream firms. These benefits are sensitive to downstream competitive pressures, yielding a potentially non-monotonic relationship between competition and integration.
Perirenal fat invasion on renal cell carcinoma: evaluation with multidetector CT

Poster: "ECR 2013 / C-0826 / Perirenal fat invasion on renal cell carcinoma: evaluation with multidetector CT" by: "A. Tsili, A. Goussia, A. Ntorkou, A. Ntoulia, D. Giannakis, L. G. Astrakas, N. Sofikitis, V. Malamou-Mitsi, M. Argyropoulou; Ioannina/GR"
Effectivity of intraoperative adjustable suture technique in horizontal strabismus.

AIM To compare the long-term effectivity of intraoperative adjustable suture technique with traditional non-adjustable strabismus surgery. METHODS Two hundred and thirty-three patients, who underwent strabismus surgery either with traditional procedures or one-stage intraoperative adjustable suture technique, were included in our long-term follow-up study. One hundred and eighteen patients were evaluated in traditional surgery group (TSG) and 115 who underwent adjustable suture were in the one-stage intraoperative adjustable surgery group (ASG). In this group 9 patients had paralytic strabismus and 16 had reoperations, 2 patients had restrictive strabismus related to thyroid eye disease. The mean follow up in the TSG was 26.2 months and it was 24.8 months in the ASG group. RESULTS In patients with exotropia (XT) the mean correction of deviation for near fixation in ASG (32.4±13.2PD) and in TSG (26.4±8.2PD) were similar (P=0.112). The correction for distant fixation in ASG (33.2±11.4PD) and TSG (30.9±7.2PD) were not significantly different (P=0.321). In patients with esotropia (ET) even the mean correction of deviation for both near (31±12PD) and distant (30.6±12.8PD) fixations were higher in ASG than in TSG, for both near (28.27±14.2PD) and distant (28.9±12.9PD) fixations, the differences were not significant (P=0.346, 0.824 respectively). The overall success rate of XT patient was 78.9% in TSG and 78.78% in ASG, the difference was not significant (P=0.629). The success rates were 78.75% in TSG and 75.51% in ASG in ET patient, which was also not significantly different (P=0.821). CONCLUSION Although patients in ASG had more complex deviation such as paralysis, reoperations and restrictive strabismus, success rates of this tecnique was as high as TSG which did not contain complicated deviation. One-stage intraoperative adjustable suture technique is a safe and effective method for cooperative patient who has complex deviation.
Pyruvate Carboxylase Activity in Primary Cultures of Astrocytes and Neurons

Abstract: The activity of the pyruvate carboxylase was determined in brains of newborn and adult mice as well as primary cultures of astrocytes, of cerebral cortex neurons, and of cerebellar granule cells. The activity was found to be 0.25 ± 0.14, 1.24 ± 0.07, and 1.75 ± 0.13 nmol min−1 mg−1 protein in, respectively, neonatal brain, adult brain, and astrocytes. Neither of the two types of neurons showed any detectable enzyme activity (i.e., < 0.05 nmol min−1 mg−1). It is therefore concluded that pyruvate carboxylase is an astrocytic enzyme.
Expanding the role of umbilical cord blood transplantation

Umbilical cord blood has become a valuable alternative source of haematopoietic stem cells for allogeneic transplantation. However, largely because of the impact of cell dose on engraftment, risk of transplant‐related mortality and survival, progress in the field has been largely restricted to children. Nevertheless, substantial clinical experience with umbilical cord blood transplantation clearly establishes its safety and effectiveness in young patients with a variety of malignant and non‐malignant diseases. Although less well established in adults, new strategies are now being explored to address the obstacle of cell dose. This article reviews the state of the art and future directions with umbilical cord blood as a source of haematopoietic stem cells for transplantation in both children and adults.
Radial basis function collocation method for decoupled fractional Laplacian wave equations

Decoupled fractional Laplacian wave equation can describe the seismic wave propagation in attenuating media. Fourier pseudospectral implementations, which solve the equation in spatial frequency domain, are the only existing methods for solving the equation. For the earth media with curved boundaries, the pseudospectral methods could be less attractive to handle the irregular computational domains. In the paper, we propose a radial basis function collocation method that can easily tackle the irregular domain problems. Unlike the pseudospectral methods, the proposed method solves the equation in physical variable domain. The directional fractional Laplacian is chosen from varied definitions of fractional Laplacian. Particularly, the vector Gr\"unwald-Letnikov formula is employed to approximate fractional directional derivative of radial basis function. The convergence and stability of the method are numerically investigated by using the synthetic solution and the long-time simulations, respectively. The method's flexibility is studied by considering homogeneous and multi-layer media having regular and irregular geometric boundaries.
Pineal Gland: Dibutyryl Cyclic Adenosine Monophosphate Stimulation of Labeled Melatonin Production

In organ cultures of intact rat pineal glands, N6O2'-dibutyryl adenosine 3', 5'-monophosphate stimulates the conversion of tritiated trytophan to tritiated melatonin, as does L-norepinephrine. Potential sites of stimulation of melatonin production by dibutyryl cyclic adenosine monophosphate are discussed, based on observations that the dibutyryl analog also stimulates the conversion of serotonin labeled with carbon-14 to carbon-14-labeled melatonin without altering hydroxyin-dole-O-methyl transferase activity or intracellular accumulation of serotonin labeled with carbon-14.
Open Source Software Adoption: A Technological Innovation Perspective

This research-in-progress aims to indentify the salient factors explaining adoption of open source software (OSS), as a technological innovation. The theoretical background of the paper is based on the technological innovation literature. We choose to focus on the open ERP case, as it is considered as a promising innovation for firms – especially medium firms – but open ERP also faces numerous challenges. The paper provides a framework and a method for investigation that has to be implemented.
The Residential Land Auction Market in Hong Kong: Market Share and Profitability

Abstract This paper examines the relationship between market concentration and profitability in the residential land auction market in Hong Kong. In the land auction market, competition is keen and the land acquired is arguably expensive, with the market dominated by a few companies. This paper finds that the developers tend to locate themselves in a suitable market position or strategic domains, within which they sustain competitiveness by increasing their market share. Evidence suggests that a developer would adopt the competitive strategy which adjusts its positioning in the best use of its abilities.
RNA Silencing: The Genome's Immune System

Genomes are databases sensitive to invasion by viruses. In recent years, a defense mechanism has been discovered, which turns out to be conserved among eukaryotes. The system can be compared to the immune system in several ways: It has specificity against foreign elements and the ability to amplify and raise a massive response against an invading nucleic acid. The latter property is beginning to be understood at the molecular level.
Substitutability between Government and Private Consumption in the GCC Countries: An Econometric Investigation

In this paper, we estimate direct long run elastici ty of substitution between government spending and private consumption for the GCC countries. Pane l estimates indicate that they are most likely to be substitutes. Individual country estimates ind icate that government spending is a strong substitute to private consumption in Bahrain, Qatar , UAE, a strong complements in KSA and a relatively weaker complements in Kuwait and Oman. E stimated elasticity of substitution for major components of government spending indicates mixed r esults. Public spending on education appears to be substitutes in three and complements in three other GCC countries. Public spending on health and military spending appears to be compl e ents to private consumption in most of the GCC countries. JEL classification: E6; H5