Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of phytochelatin synthase in tobacco: distinctive effects of AtPCS1 and CePCS genes on plant response to cadmium

Phytochelatins, heavy-metal-binding polypeptides, are synthesized by phytochelatin synthase (PCS) (EC 2.3.2.15). Previous studies on plants overexpressing PCS genes yielded contrasting phenotypes, ranging from enhanced cadmium tolerance and accumulation to cadmium hypersensitivity. This paper compares the effects of overexpression of AtPCS1 and CePCS in tobacco (Nicotiana tabacum var. Xanthi), and demonstrates how the introduction of single homologous genes affects to a different extent cellular metabolic pathways leading to the opposite of the desired effect. In contrast to WT and CePCS transformants, plants overexpressing AtPCS1 were Cd-hypersensitive although there was no substantial difference in cadmium accumulation between studied lines. Plants exposed to cadmium (5 and 25 μM CdCl2) differed, however, in the concentration of non-protein thiols (NPT). In addition, PCS activity in AtPCS1 transformants was around 5-fold higher than in CePCS and WT plants. AtPCS1 expressing plants displayed a dramatic accumulation of γ-glutamylcysteine and concomitant strong depletion of glutathione. By contrast, in CePCS transformants, a smaller reduction of the level of glutathione was noticed, and a less pronounced change in γ-glutamylcysteine concentration. There was only a moderate and temporary increase in phytochelatin levels due to AtPCS1 and CePCS expression. Marked changes in NPT composition due to AtPCS1 expression led to moderately decreased Cd-detoxification capacity reflected by lower SH:Cd ratios, and to higher oxidative stress (assessed by DAB staining), which possibly explains the increase in Cd-sensitivity. The results indicate that contrasting responses to cadmium of plants overexpressing PCS genes might result from species-dependent differences in the activity of phytochelatin synthase produced by the transgenes.
SPIRIT: Sequential Pattern Mining with Regular Expression Constraints

Discovering sequential patterns is an important problem in data mining with a host of application domains including medicine, telecommunications, and the World Wide Web. Conventional mining systems provide users with only a very restricted mechanism (based on minimum support) for specifying patterns of interest. In this paper, we propose the use of Regular Expressions (REs) as a flexible constraint specification tool that enables user-controlled focus to be incorporated into the pattern mining process. We develop a family of novel algorithms (termed SPIRIT ‐ Sequential Pattern mIning with Regular expressIon consTraints) for mining frequent sequential patterns that also satisfy user-specified RE constraints. The main distinguishing factor among the proposed schemes is the degree to which the RE constraints are enforced to prune the search space of patterns during computation. Our solutions provide valuable insights into the tradeoffs that arise when constraints that do not subscribe to nice properties (like anti-monotonicity) are integrated into the mining process. A quantitative exploration of these tradeoffs is conducted through an extensive experimental study on synthetic and real-life data sets.
Narrative Inquiry

At least once a year, I teach a graduate course titled Narrative Inquiry. At the beginning of the course I always inform students that they will not likely learn how to do narrative inquiry in the narrative inquiry course. Instead they will interrogate the strategies, purposes, practices, and challenges of narrative inquiry, and they will learn how complicated, even messy, the whole business of narrative inquiry really is. I organize the course around an investigation of three principal dynamics involved in narrative inquiry: story, interpretation, and discourse. I invite students to consider matters related to story and interpretation, but I encourage them especially to attend to the art of discourse.
A Manifesto for Future Generation Cloud Computing: Research Directions for the Next Decade

The Cloud computing paradigm has revolutionised the computer science horizon during the past decade and has enabled the emergence of computing as the fifth utility. It has captured significant attention of academia, industries, and government bodies. Now, it has emerged as the backbone of modern economy by offering subscription-based services anytime, anywhere following a pay-as-you-go model. This has instigated (1) shorter establishment times for start-ups, (2) creation of scalable global enterprise applications, (3) better cost-to-value associativity for scientific and high performance computing applications, and (4) different invocation/execution models for pervasive and ubiquitous applications. The recent technological developments and paradigms such as serverless computing, software-defined networking, Internet of Things, and processing at network edge are creating new opportunities for Cloud computing. However, they are also posing several new challenges and creating the need for new approaches and research strategies, as well as the re-evaluation of the models that were developed to address issues such as scalability, elasticity, reliability, security, sustainability, and application models. The proposed manifesto addresses them by identifying the major open challenges in Cloud computing, emerging trends, and impact areas. It then offers research directions for the next decade, thus helping in the realisation of Future Generation Cloud Computing.
Selective switching median filter for the removal of salt & pepper impulse noise

In this paper, a new median based filtering algorithm is presented for the removal of impulse noise from digital images. A good analysis of the limitations of the top ranking median filters, the progressive switching median filter, PSMF and the rank-order based adaptive median filter, RAMF is made and are overcome very effectively by the proposed filter which cleans the impulse corruptions of a digital image in two distinct phases of impulse detection and impulse correction. The detection phase identifies the corrupted pixels into a flag image by a spatial rank ordered approach and the correction phase modifies the corrupted pixels identified in the flag image by a more suitable rank ordered value by considering the neighboring features. The filter shows better performance than most other impulse filters, and in particular, that of the top ranking RAMF and PSMF in terms of computational aspect and objectively. The filtering technique gives good results with less patchy effects from images corrupted at higher noise levels and the results are more appealing with good fidelity at lower noise levels
virF-Positive Yersinia pseudotuberculosis and Yersinia enterocolitica Found in Migratory Birds in Sweden

ABSTRACT During spring and autumn migrations, 468 fecal samples from 57 different species of migratory birds were collected in Sweden. In total, Yersinia spp. were isolated from 12.8% of collected samples. The most commonly found species was Yersinia enterocolitica, which was isolated from 5.6% of all collected samples, followed by Y. intermedia (3.8%), Y. frederiksenii (3.0%), Y. kristensenii (0.9%), Y. pseudotuberculosis (0.6%), and Y. rohdei (0.4%). The pathogenic, virF-positive Y. pseudotuberculosis strains were recovered from three thrushes. These strains belonged to the same bioserotype, 1/O:2, but had two different profiles as determined by pulsed-field gel electrophoresis with NotI and SpeI enzymes. In addition, 10 Y. enterocolitica strains, all from barnacle geese, belonged to bioserotype 3/O:3, which is associated with human disease. Two of the strains were pathogenic, carrying the virF gene on their plasmids. All pathogenic Y. pseudotuberculosis and Y. enterocolitica strains were recovered during the spring, and as the birds were caught during active migration they likely became infected at an earlier stage of the migration, thus potentially transporting these bacterial pathogens over long geographical distances.
Book reviews

Reviewed book: 'European Spatial Planning and Territorial Cooperation' by Stefanie Duehr, Claire Colomb & Vincent Nadin, 2010, Abingdon and New York, Routledge, 460 pp., ISBN 978-0-415-46774-2, £34.99 (pbk)
Exploiting Scope for Shallow Discourse Parsing

We present an approach to automatically identifying the arguments of discourse connectives based on data from the Penn Discourse Treebank. Of the two arguments of connectives, called Arg1 and Arg2, we focus on Arg1, which has proven more challenging to identify. Our approach employs a sentence-based representation of arguments, and distinguishes ""intra-sentential connectives"", which take both their arguments in the same sentence, from ""inter-sentential connectives"", whose arguments are found in different sentences. The latter are further distinguished by paragraph position into ""ParaInit"" connectives, which appear in a paragraph-initial sentence, and ""ParaNonInit"" connectives, which appear elsewhere. The paper focusses on predicting Arg1 of Inter-sentential ParaNonInit connectives, presenting a set of scope-based filters that reduce the search space for Arg1 from all the previous sentences in the paragraph to a subset of them. For cases where these filters do not uniquely identify Arg1, coreference-based heuristics are employed. Our analysis shows an absolute 3% performance improvement over the high baseline of 83.3% for identifying Arg1 of Inter-sentential ParaNonInit connectives.
G6b-B Inhibits Constitutive and Agonist-induced Signaling by Glycoprotein VI and CLEC-2*S⃞

Platelets play an essential role in wound healing by forming thrombi that plug holes in the walls of damaged blood vessels. To achieve this, platelets express a diverse array of cell surface receptors and signaling proteins that induce rapid platelet activation. In this study we show that two platelet glycoprotein receptors that signal via an immunoreceptor tyrosine-based activation motif (ITAM) or an ITAM-like domain, namely the collagen receptor complex glycoprotein VI (GPVI)-FcR γ-chain and the C-type lectin-like receptor 2 (CLEC-2), respectively, support constitutive (i.e. agonist-independent) signaling in a cell line model using a nuclear factor of activated T-cells (NFAT) transcriptional reporter assay that can detect low level activation of phospholipase Cγ (PLCγ). Constitutive and agonist signaling by both receptors is dependent on Src and Syk family kinases, and is inhibited by G6b-B, a platelet immunoglobulin receptor that has two immunoreceptor tyrosine-based inhibitory motifs in its cytosolic tail. Mutation of the conserved tyrosines in the two immunoreceptor tyrosine-based inhibitory motifs prevents the inhibitory action of G6b-B. Interestingly, the inhibitory activity of G6b-B is independent of the Src homology 2 (SH2)-domain containing tyrosine phosphatases, SHP1 and SHP2, and the inositol 5′-phosphatase, SHIP. Constitutive signaling via Src and Syk tyrosine kinases is observed in platelets and is associated with tyrosine phosphorylation of GPVI-FcR γ-chain and CLEC-2. We speculate that inhibition of constitutive signaling through Src and Syk tyrosine kinases by G6b-B may help to prevent unwanted platelet activation.
Endoscopic tri-modal imaging for surveillance in ulcerative colitis: randomised comparison of high-resolution endoscopy and autofluorescence imaging for neoplasia detection; and evaluation of narrow-band imaging for classification of lesions

Background: Endoscopic tri-modal imaging (ETMI) incorporates white light endoscopy (WLE), autofluorescence imaging (AFI) and narrow-band imaging (NBI). Aims: To assess the value of ETMI for the detection and classification of neoplasia in patients with longstanding ulcerative colitis. Design: Randomised comparative trial of tandem colonoscopies. Setting: Academic Medical Centre Amsterdam, Netherlands. Patients and methods: Fifty patients with ulcerative colitis underwent surveillance colonoscopy with ETMI. Each colonic segment was inspected twice, once with AFI and once with WLE, in random order. All detected lesions were inspected by NBI for Kudo pit pattern analysis and additional random biopsies were taken. Main outcome measures: Neoplasia miss-rates of AFI and WLE, and accuracy of the Kudo classification by NBI. Results: Among patients assigned to inspection with AFI first (n = 25), 10 neoplastic lesions were primarily detected. Subsequent WLE detected no additional neoplasia. Among patients examined with WLE first (n = 25), three neoplastic lesions were detected; subsequent inspection with AFI added three neoplastic lesions. Neoplasia miss-rates for AFI and WLE were 0% and 50% (p = 0.036). The Kudo classification by NBI had a sensitivity and specificity of 75% and 81%; however, all neoplasia was coloured purple on AFI (sensitivity 100%). No additional patients with neoplasia were detected by random biopsies. Conclusion: Autofluorescence imaging improves the detection of neoplasia in patients with ulcerative colitis and decreases the yield of random biopsies. Pit pattern analysis by NBI has a moderate accuracy for the prediction of histology, whereas AFI colour appears valuable in excluding the presence of neoplasia. Trial registration number: ISRCTN05272746
Post traumatic stress and debriefing in the emergency services.

The following theseis is divided into three separate parts. Part one is a review of the current post traumatic stress literature. The review outlines the development of the study of post-traumatic stress from early wartime observations to the current focus on the effects of disaster on both victims and emergency personnel. A number of theoretical conceptualisations are offered to describe how a proportion of those exposed to catastrophic events subsequently develop a variety of disabling conditions. Implications for treatment are discussed, emphasising the need for preventative and proactive interventions. Finally, an alternative adaptive model of PTSD is described in the context for future recommendations. Part two of the thesis describes a study to explore the factors associated with psychological distress in emergency workers following involvement in critical incidents and to determine the efficacy of psychological debriefing in the alleviation of such distress. The study demonstrates that workers initially experience some distress as a response to their work, but that this is typically short lived. Important factors in predicting distress are poor social support, knowing the incident victim and if the incident occurred over both
Capillaries in the epithelium of pterygium

AIM To present new morphological observations of intraepithelial capillaries in pterygium and to provide some explanations for this phenomenon. METHODS The ultrastructural features of pterygia from 26 patients were examined. Surgically excised tissue was processed for conventional light and transmission electron microscopy. RESULTS Individual capillaries within the epithelium of the anterior half towards the head of pterygia were identified in 11 specimens out of 26 pterygia examined (42.3%). The perivascular connective tissue of the intraepithelial capillaries contained fibroblasts, collagen fibrils, and elastin-like material. Epithelial cells surrounding these capillaries showed defects in the basal lamina in contrast with the continuous basal lamina of the endothelium. In the intercellular space of the epithelium an amorphous substance, occasional fibroblast processes, and collagen fibrils were frequently observed. CONCLUSION Capillaries in the epithelium of pterygia are rare, but not exceptional. The ingrowth of these vessels from the stroma into the epithelium can be interpreted as a reaction to hypoxia or deficiency of any other substance transported via the bloodstream. Apparently, the perivascular connective tissue can be used by ingrowing fibroblasts as a migration pathway. The migrating fibroblasts appear to use the defects of the epithelial basal lamina (whether partially or complete) in order to reach the intercellular space. It is possible that collagen fibrils in the epithelial intercellular space have been laid down by fibroblasts which contribute to the pathological dedifferentiation of the conjunctival epithelium.
Modelling Multiple Sclerosis In Vitro and the Influence of Activated Macrophages

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). The prevalence of MS is approximately 2 million people worldwide, with an incidence of about 1:1000 in Europe and Northern America, and women are affected more often compared to men, at a ratio of approximately 2:1. It is the most common cause of neurological disability among young adults with an onset generally between 20 and 40 years of age [Pugliatti et al., 2002]. The major neuropathological hallmarks of MS are demyelinating lesions associated with perivascular infiltrates, consisting of macrophages/microglia and lymphocytes. The lesions are characterized by destruction of myelin sheaths, oligodendrocyte death, axonal damage and glial scar formation, called astrogliosis. Demyelination is a central event in MS pathology. Although some remyelination occurs, it ultimately fails [Franklin, 2002]. The cause of the remyelination failure is not clear, although several processes have been suggested to play a role [Franklin and Ffrench-Constant, 2008; Wolswijk, 2002; John et al., 2002]. Not only processes behind remyelination failure remain elusive, also the cellular mechanisms behind the demyelination and axonal damage are largely unknown. Modelling MS both in animals and in vitro could help with understanding this. This chapter will focus on MS pathology and the models that exist for investigating this disease, especially zooming in on in vitro models.
IL-28A (IFN-λ2) modulates lung DC function to promote Th1 immune skewing and suppress allergic airway disease

IL‐28 (IFN‐λ) cytokines exhibit potent antiviral and antitumor function but their full spectrum of activities remains largely unknown. Recently, IL‐28 cytokine family members were found to be profoundly down‐regulated in allergic asthma. We now reveal a novel role of IL‐28 cytokines in inducing type 1 immunity and protection from allergic airway disease. Treatment of wild‐type mice with recombinant or adenovirally expressed IL‐28A ameliorated allergic airway disease, suppressed Th2 and Th17 responses and induced IFN‐γ. Moreover, abrogation of endogenous IL‐28 cytokine function in IL‐28Rα−/− mice exacerbated allergic airway inflammation by augmenting Th2 and Th17 responses, and IgE levels. Central to IL‐28A immunoregulatory activity was its capacity to modulate lung CD11c+ dendritic cell (DC) function to down‐regulate OX40L, up‐regulate IL‐12p70 and promote Th1 differentiation. Consistently, IL‐28A‐mediated protection was absent in IFN‐γ−/− mice or after IL‐12 neutralization and could be adoptively transferred by IL‐28A‐treated CD11c+ cells. These data demonstrate a critical role of IL‐28 cytokines in controlling T cell responses in vivo through the modulation of lung CD11c+ DC function in experimental allergic asthma.
Towards an Examination of Error Related Neural Processes in Real-World Tasks: ERP Evidence of Uncertainty, Expectancy, Difficulty and Anxiety

In four experiments I addressed factors that affect human performance monitoring as indicated by neural correlates observed in response-locked event related potentials. Specifically, I examined modulations of the error related negativity (ERN), the correct response negativity (CRN), and the error positivity (Pe) components across a variety of conditions. These components, all thought to be generated in the anterior cingulate cortex, represent activation of the performance monitoring system. Experiments 1 and 2 used stimulus congruency and visual noise to manipulate response and stimulus uncertainty in an extension of previous research. These manipulations, together with a between experiment task manipulation, examined the role of cognitive/attentional load in performance monitoring. Replication ofprevious findings and a task specific modulation of ERN amplitudes provided support for a role of cognitive load in performance monitoring. Further, these two experiments used a novel task and novel stimuli to replicate previous research and extend our knowledge of how uncertainty affects performance monitoring. In stark comparison to all previous research in this area, Experiments 3 and 4 both employed complex and somewhat ecologically valid tasks. Standard ERN/Pe results in Experiment 3 (touch typing task) revealed that it is possible to examine the ERN in more complex, real world-like tasks. Further, an expectancy manipulation elicited marginal differences in the response-locked Pe but resulted in large NI and P3 differences suggesting a possible role of attention in early expectation driven performance monitoring adjustments. Experiment 4 examined the role of task difficulty, anxiety level and exposure (i.e., time on task) for effects on ERN and Pe amplitudes. By
Communicating Climate Change: Are Stories Better than “Just the Facts”?

Postpositive policy scholarship has long asserted the importance of narratives—or stories—in shaping public policy through public opinion. In part, the Narrative Policy Framework (NPF) was developed to empirically test this assertion. To assess the relationship between policy narratives and public opinion, NPF posits several causal mechanisms including narrative transportation. Narrative transportation is a measure used to assess the extent to which individuals exposed to a story are “transported” into that story. NPF hypothesizes that as narrative transportation increases the reader of the story will (i) have more positive affect for characters within the story; and (ii) will find the story more persuasive. Using an online experiment involving a nationally representative sample of over 1,700 respondents, this research tests narrative transportation hypotheses by exposing subjects to one of three Cultural Theory narratives about climate change, as well as a control list of scientifically agreed upon facts. While findings do not support that narratives are any more transportive than fact lists in terms of directly persuading respondents to accept specific climate change policies, the data do show that narrative transportation positively influences affect for hero characters, which extant research demonstrates indirectly influences the persuasiveness of a story.
The Preferences Scale: Multinational Assessment of a New Measure of Morningness

Several self-report scales have been developed to measure morningness, or the preference for early morning or late evening activity (i.e., larks vs. owls). This individual difference in human circadian (time-of-day) rhythms has applications in the selection and placement of shiftworkers for night work in industry. Researchers have recently questioned the suitability of existing scales for people with alternate sleep-wake schedules and lifestyles. These factors may also render existing scales inappropriate for use in some cultures. To address this deficiency, we developed a new morningness scale (the preferences scale) that is not yoked to specific times of the 24-hour day and has a simplified response format. Data on the preferences scale were collected from university students (total N=1,212) in four countries (U.S., England, Holland, and Spain). Responses on external validity measures (self-rated alertness over the waking day and actual and preferred arise and bed times) and another morningness scale (for comparative purposes) were also collected. Although scale statistics (aggregate and by country) suggest that the psychometric properties of the preferences scale were adequate, scale mean differences existed across countries. These results may indicate cultural, as well as the established biological, differences in morningness. However, a more thorough psychometric assessment is needed to substantiate this possibility.