Miracle-dz/UniFAR-FTUs huggingface dataset:
C‐di‐GMP: the dawning of a novel bacterial signalling system

Bis‐(3′‐5′)‐cyclic dimeric guanosine monophosphate (c‐di‐GMP) has come to the limelight as a result of the recent advances in microbial genomics and increased interest in multicellular microbial behaviour. Known for more than 15 years as an activator of cellulose synthase in Gluconacetobacter xylinus, c‐di‐GMP is emerging as a novel global second messenger in bacteria. The GGDEF and EAL domain proteins involved in c‐di‐GMP synthesis and degradation, respectively, are (almost) ubiquitous in bacterial genomes. These proteins affect cell differentiation and multicellular behaviour as well as interactions between the microorganisms and their eukaryotic hosts and other phenotypes. While the role of GGDEF and EAL domain proteins in bacterial physiology and behaviour has gained appreciation, and significant progress has been achieved in understanding the enzymology of c‐di‐GMP turnover, many questions regarding c‐di‐GMP‐dependent signalling remain unanswered. Among these, the key questions are the identity of targets of c‐di‐GMP action and mechanisms of c‐di‐GMP‐dependent regulation. This review discusses phylogenetic distribution of the c‐di‐GMP signalling pathway in bacteria, recent developments in biochemical and structural characterization of proteins involved in its metabolism, and biological processes affected by c‐di‐GMP. The accumulated data clearly indicate that a novel ubiquitous signalling system in bacteria has been discovered.
Development of Lensed Color Filter technology for higher SNR and lower crosstalk CMOS image sensor

To enhance SNR performance by reducing crosstalk in backside illumination (BSI) pixel structure of CMOS image sensor, a new process technology, named as ‘lensed color filter’, was developed. Effective color filter thickness is increased while optical height is lower than conventional structure. The real chip with 1.12um pixels and 12Mega resolution was manufactured. It has 25% higher color filter thickness and 15% lower optical stack. Evaluation shows that SNR10 performance is improved by 10% and crosstalk is reduced by 11%.
Winds of change in Sarawak politics

The RSIS Working Paper series presents papers in a preliminary form and serves to stimulate comment and discussion. The views expressed are entirely the author’s own and not that of the S. Rajaratnam School of International Studies. If you have any comments, please send them to the following email address: isjwlin@ntu.edu. sg. Unsubscribing If you no longer want to receive RSIS Working Papers, please click on “Unsubscribe. ” to be removed from the list.
Experiments in apply morphological analysis in speech recognition and their cognitive explanation

On the other hand, there is much evidence that human listeners are sensitive to the internal structure of words, particularly to that related to their meaning, or morphology. Some evidence for this is just to do with the production and interpretation of novel, morphologically complex words such as “un-micro-wave-ability”. But there is also interesting psycholinguistic evidence that morphological analysis is performed on-line during the processes of word recognition of common words. This seems to be the case for both inflexional morphology (cows, milked) and derivational morphology (distrust, government).
β1-6 branching of cell surface glycoproteins may contribute to uveal melanoma progression by up-regulating cell motility

Purpose This study investigated the influence of integrin expression as well as the oligosaccharide structure of surface N-glycoproteins on cell behavior of two primary uveal (92–1 and Mel202) and two primary cutaneous (FM55P and IGR-39) melanoma cell lines. Methods Cell adhesion to fibronectin and cell migration on fibronectin (wound healing) were selected as the studied cell behavior parameters. The percentage of cells positive for expression of selected integrins was estimated by flow cytometric analysis. The influence of β1–6 branched complex-type N-oligosaccharides on wound healing on fibronectin was investigated. Cell surface β1–6 branched N-oligosaccharides were measured by their specific binding to PHA-L followed by flow cytometry, and the fibronectin receptors bearing β1–6 GlcNAc branched N-linked glycans were identified. In addition, the transcript of GnT-V (the enzyme that catalyzes the addition of N-acetylglucosamine to the core mannose of di- and tri-antennary N-glycans through a β1–6 linkage) was analyzed by semiquantitative RT–PCR. Results Unlike the two examined cutaneous melanoma cell lines, neither of the uveal melanoma cells adhered to fibronectin. The adhesion efficiency of IGR-39 cells was twice that of FM55P cells. In contrast, uveal melanoma cells repaired scratch wounds on fibronectin-coated surfaces twice as fast as cutaneous melanoma cells did. The expression of α3β1, α4β1, α5β1, and αvβ3 integrins, acting as fibronectin receptors, differed between the tested cell lines, and no distinct pattern distinguished uveal melanoma from cutaneous melanoma except for high expression of α4β1 integrin on both FM55P and IGR-39 cells. The results also demonstrated that the high levels of α3β1, α4β1, and α5β1 integrin expression on IGR-39 cells promoted their strong attachment to fibronectin-coated surfaces. In addition, 92–1, Mel202, and FM55P cells showed no or low adhesion to fibronectin, perhaps the result of low expression of fibronectin receptors excluding high expression of α4β1 integrin in FM55P cells. Cell migration was significantly decreased in three out of four PHA-L-treated cell lines, suggesting that β1–6 branched complex type N-oligosaccharides are critical for 92–1, Mel202, and FM55P cell motility. Semiquantitative RT–PCR analysis showed that the tested cells did not differ in mRNA levels of β1–6 –N-acetylglucosaminyltransferase V. However, FACS analysis showed that 92–1, Mel202 and IGR-39 cells expressed significantly higher amounts of β1–6 branched N-oligosaccharides on the cell surface than FM55P cells did. All examined α3, α5, αv, and β1 integrin subunits were shown to bear β1–6 branched N-linked glycans. Conclusions The role of integrins and their N-glycosylation in the regulation of uveal melanoma growth and progression is largely unknown. These results reveal that cell surface complex-type N-glycans with GlcNAc β1–6 branches are important factors determining the migration of primary uveal melanoma cells on fibronectin.
Iron Metabolism and Malaria

Recent evidence from a large, randomized, controlled trial has suggested that the universal administration of iron to children in malaria-endemic areas is associated with an increase in adverse health outcomes. The purpose of this paper is to summarize the available ecologic and intervention trials related to iron and malaria in children, and to set these against current knowledge of the biology of host–pathogen interactions involving iron metabolism. We conclude that, although not fully consistent, the balance of evidence confirms that administration of iron (usually in combination with folic acid) increases the incidence of malaria when given without prophylaxis and in the absence of universal access to treatment. The mechanisms by which additional iron can benefit the parasite are far from clear. There is evidence to suggest that the apparent detrimental effect of iron supplementation may vary according to levels of antecedent iron status, the presence of hemoglobinopathies and glucose-6-phosphate dehydrogenase (G6PD) deficiency, and other host genetic variants, such as variants in haptoglobin. The effects of malaria on host iron metabolism are also reviewed and reveal that the key cause of malaria-induced anemia is a maldistribution of iron and suppression of erythropoiesis rather than an exacerbation of gross iron deficiency. We tentatively conclude that, if it is to be recommended, universal iron supplementation in malarious areas should only be considered in conjunction with some form of prophylaxis (e.g., intermittent preventive therapy [IPT]) or in the context of good health services with ready access to facilities for malaria diagnosis and treatment. An alternative approach would be to screen for anemia and target supplementation only to anemic children. With regard to treatment, there is good evidence that iron supplementation should be withheld until the treatment schedule is complete, both because iron may inhibit treatment and because the absorption of oral iron is blocked by the inflammatory response.
Seqüências de (sibilante + consoante) no português de Belo Horizonte

This paper investigates cases of sound variation involving sequences of (sibilant + consonant) in Brazilian Portuguese (BP). Emphasis is given to the analysis of alveolar (sibilant + stop) sequences as in the word – festa [EfEsta] – and to the alveopalatal (sibilant + affricate)sequences – as in the word triste [EtRiStSi]. The cases of variation we will be dealing with involve the loss of the stop or the affricate where only the sibilant is manifested: festa ‘party ‘ [EfEsta] a [EfEsa]and triste ‘sad’ [EtRiStSi] a [EtRiSi]. This paper evaluates the role of phonetic properties as potential motivation for the variation:agreement of place of articulation and also agreement of voicing for the consonants in the sequence is considered. The fact that the sequences involved in the variation are related to a complex syllable pattern – that is, (coda-onset) – will also be explored. Some structural aspects which may condition the phenomena will be addressed:stress placement and the quality of the vowel which precedes the(coda-onset) sequence. It will be suggested that the lack of conditioning structural factors leads us to evaluate this case of variation within the Lexical Diffusion model (WANG, 1969). Lexical Diffusion appears to be the most appropriate approach to analyse the phenomena addressed in this paper, since it accounts for the . different behaviour of some structurally similar sequences. Finally,the paper indicates some aspects to be pursued in future research.
Do not wake sleeping dogs: Pay-out policies in founding family firms

This article examines founding family influence on pay-out policies for Swiss listed firms over the period 2003-2010. We find that founding family firms have higher dividends and total pay-outs than non-family firms. There is no significant difference between stock repurchases for the two types of firms. We show that specific firm characteristics such as active involvement of family members, the presence of only one or multiple family members or the existence of a second blockholder play an important role for pay-out policies in family firms. Firms using control enhancing mechanisms do not have significantly lower pay-outs. We propose three possible explanations for the observed pay-out policies: private benefit extraction, reputation building, and family legacy. Our findings appear to be consistent with the reputation building hypothesis.
Retroviral Vectors: Post Entry Events and Genomic Alterations

The curative potential of retroviral vectors for somatic gene therapy has been demonstrated impressively in several clinical trials leading to sustained long-term correction of the underlying genetic defect. Preclinical studies and clinical monitoring of gene modified hematopoietic stem and progenitor cells in patients have shown that biologically relevant vector induced side effects, ranging from in vitro immortalization to clonal dominance and oncogenesis in vivo, accompany therapeutic efficiency of integrating retroviral gene transfer systems. Most importantly, it has been demonstrated that the genotoxic potential is not identical among all retroviral vector systems designed for clinical application. Large scale viral integration site determination has uncovered significant differences in the target site selection of retrovirus subfamilies influencing the propensity for inducing genetic alterations in the host genome. In this review we will summarize recent insights gained on the mechanisms of insertional mutagenesis based on intrinsic target site selection of different retrovirus families. We will also discuss examples of side effects occurring in ongoing human gene therapy trials and future prospectives in the field.
The Na+/H+ exchanger SOS1 controls extrusion and distribution of Na+ in tomato plants under salinity conditions

Maintaining a high K+/Na+ ratio in the cell cytosol, along with the transport processes implicated in the xylem and phloem loading/unloading of Na+ in plants (long-distance transport) are key aspects in plant salt tolerance. The Ca2+-dependent SOS pathway regulating Na+ and K+ homeostasis and long-distance Na+ transport has been reported in Arabidopsis. However, Arabidopsis might not be the best model to analyze the involvement of the SOS pathway in long-distance Na+ transport due to the very short stem of these plants which do not allow a precise dissection of the relative content of Na+ in stem versus leaf. This separation would be critical to assess the role of SOS1 in xylem loading/unloading, Na+ export by roots, retention in stems and the differential distribution/accumulation in old leaves. Towards this goal, tomato might represent a superior model due to its anatomical structure and agricultural significance. We recently demonstrated the key role played by the plasma membrane Na+/H+ antiporter SlSOS1 in salt tolerance in tomato by maintaining ion homeostasis under salinity stress and in the partitioning of Na+ in plant organs.
Effects of antihypertensive agents on baroreceptor function in early hypertensive rats.

To investigate the effects of antihypertensive treatment with four currently used agents (trichlormethiazide, atenolol, nicardipine, and enalapril) on the arterial baroreceptor function at the early phase of hypertension, we administered the agents to spontaneously hypertensive rats and Wistar-Kyoto rats from 8 to 10 weeks of age and examined the aortic nerve activity function. In untreated spontaneously hypertensive rats, the relation between the arterial pressure and aortic nerve activity was shifted to the right, that is, to a higher pressure level (threshold pressure, 90 +/- 3 versus 76 +/- 1 mm Hg, P < .05), and the maximum gain which was obtained by logistic function analysis was depressed (1.55 +/- 0.08% versus 2.18 +/- 0.13% maximum/mm Hg, P < .01) as compared with untreated Wistar-Kyoto rats. An equivalent decrease in arterial pressure with each of the four agents (-20 +/- 1 mm Hg, P < .01) produced a leftward shift of the arterial pressure-aortic nerve activity relation to a similar extent (threshold pressure, 77 +/- 1 mm Hg, P < .05) in spontaneously hypertensive rats. In addition, treatment with the four agents equally augmented the maximum gain in spontaneously hypertensive rats (2.13 +/- 0.09% maximum/mm Hg, P < .05). The antihypertensive agents affected neither the blood pressure nor the aortic nerve activity in Wistar-Kyoto rats. These findings suggest that antihypertensive treatment with the four classes of agents equally enhances the arterial baroreceptor function through blood pressure reduction but not through specific depressor mechanisms at the early stage of hypertension.
Quantitative MRI of the brain : measuring changes caused by disease

Contributors.Reviewers. Foreward.Introduction. Section A: The Measurement Process.1. Concepts: Measurement and MR (Paul S. Tofts). 2. The Measurement Process: MR Data Collection and Image Analysis (Paul S. Tofts). 3. QA: Quality Assurance, Accuracy, Precision and Phantoms (Paul S. Tofts). Section B: Windows into the Brain: Measuring MR Parameters.4. PD: Proton Density of Tissue Water (Paul Tofts). 5. T1: the Longitudinal Relaxation Time (Penny A. Gowland and Valerie L. Stevenson). 6. T2: the Transverse Relaxation Time (Philip A. Boulby and Fergus J. Rugg-Gunn). 7. D: the Diffusion of Water (Claudia A.M. Wheeler-Kingshott, Gareth J. Barker, Stefan C.A. Steens and Mark A. van Buchem). 8. MT: Magnetisation Transfer (Paul S. Tofts, Stefan C.A. Steens and Mark A. van Buchem). 9. Spectroscopy: 1H Metabolite Concentrations (Paul S. Tofts and Adam D. Waldman). 10. T1-w DCE-MRI: T1-weighted Dynamic Contrast-enhance d MRI (Geoff J.M. Parker and Anwar Padhani). 11. T2- and T2-w DCE-MRI: Blood Perfusion and Volume Estimation using Bolus Tracking (Richard P. Kennan and H. Rolf Ja ger). 12. Functional MRI (Peter Jezzard and Nick F. Ramsay). 13. ASL: Blood Perfusion Measurements using Arterial Spin Labelling (Laura M. Parkes, John A. Detre). Section C: The Biology.14. Biology: The Significance of MR Parameters in Multiple Sclerosis (Bruno Brochet, Klaus G. Petry and Vincent Dousset). Section D: Analysing Images.15. Spatial Registration of Images (John Ashburner and Catriona D. Good). 16. Volume and Atrophy (Geoff J.M. Parker and Declan T. Chard). 17. Shape and Texture (William R. Crum). 18. Histograms: Measuring Subtle Diffuse Disease (Paul S. Tofts, Gerard R. Davies and Jamshid Dehmeshki ). Section E: Where are we going? 19. The Future of qMRI: Conclusions and Speculation (Paul S. Tofts). Appendix 1: Greek Alphabet for Scientific Use.Index.
Image segmentation via IB method

This paper presents an image segmentation algorithm, called ISIB, based on the Information Bottleneck (IB) method. ISIB extracts the image patterns by maximally preserving the mutual information between the segments and the gray scale values. There are two stages in our algorithm, partitioning the image and merging the segmentations. In the partition process, we segment an image by maximizing the mutual information gain, so that the fine structure of the image can be obtained. In the second stage, we use the density based IB method to merge the fine segments to get the whole structure of the image. Our experiments show that, compared with other advanced image segment methods, ISIB induces the contours which better describe image objects.
Local Nonstationarity for Efficient Bayesian Optimization

Bayesian optimization has shown to be a fundamental global optimization algorithm in many applications: ranging from automatic machine learning, robotics, reinforcement learning, experimental design, simulations, etc. The most popular and effective Bayesian optimization relies on a surrogate model in the form of a Gaussian process due to its flexibility to represent a prior over function. However, many algorithms and setups relies on the stationarity assumption of the Gaussian process. In this paper, we present a novel nonstationary strategy for Bayesian optimization that is able to outperform the state of the art in Bayesian optimization both in stationary and nonstationary problems.
Poetic Effects: A Relevance Theory Perspective

1. Acknowledgements 2. Introduction 3. 1. Literary studies and literary theory 4. 2. Theories of literariness, language and communication in literary studies 5. 3. Pragmatic Theory 6. 4. Metaphor 7. 5. Schemes and verse effects 8. 6. Emotion, attitude and sentimentality 9. 7. Varieties of affective experience 10. 8. Conclusion 11. References 12. Index of Names 13. Index of Subjects
The case for addressing gender and power in sexuality and HIV education: a comprehensive review of evaluation studies.

CONTEXT Curriculum-based sexuality and HIV education is a mainstay of interventions to prevent STIs, HIV and unintended pregnancy among young people. Evidence links traditional gender norms, unequal power in sexual relationships and intimate partner violence with negative sexual and reproductive health outcomes. However, little attention has been paid to analyzing whether addressing gender and power in sexuality education curricula is associated with better outcomes. METHODS To explore whether the inclusion of content on gender and power matters for program efficacy, electronic and hand searches were conducted to identify rigorous sexuality and HIV education evaluations from developed and developing countries published between 1990 and 2012. Intervention and study design characteristics of the included interventions were disaggregated by whether they addressed issues of gender and power. RESULTS Of the 22 interventions that met the inclusion criteria, 10 addressed gender or power, and 12 did not. The programs that addressed gender or power were five times as likely to be effective as those that did not; fully 80% of them were associated with a significantly lower rate of STIs or unintended pregnancy. In contrast, among the programs that did not address gender or power, only 17% had such an association. CONCLUSIONS Addressing gender and power should be considered a key characteristic of effective sexuality and HIV education programs.
Ultrasonography and the Ultrasound-Based Management of Thyroid Nodules: Consensus Statement and Recommendations

The detection of thyroid nodules has become more common with the widespread use of ultrasonography (US). US is the mainstay for detecting and making the differential diagnosis of thyroid nodules as well as for providing guidance for a biopsy. The Task Force on Thyroid Nodules of the Korean Society of Thyroid Radiology has developed recommendations for the US diagnosis and US-based management of thyroid nodules. The review and recommendations in this report have been based on a comprehensive analysis of the current literature, the results of multicenter studies and from the consensus of experts.
[High incidence and complications of Clostridium difficile diarrhea among patients with renal diseases].

BACKGROUND Clostridium difficile is the main agent causing antimicrobial associated nosocomial diarrhea. Chronic renal failure is a risk factor for this type of diarrhea. AIM To study the incidence and complications of Clostridium difficile diarrhea in a university hospital and among patients with renal diseases. PATIENTS AND METHODS Retrospective review of all cases of Clostridium difficile diarrhea that occurred in a university hospital, between June 2000 and May 2001. RESULTS In the Nephrology Unit, 48 episodes of Clostridium difficile diarrhea occurred in 35 patients (7 cases per 100 discharges/year). This figure is higher than the global incidence in the hospital (0.53 cases per 100 discharges/year, p < 0.001). The mean age of the 33 patients with renal diseases was 63 years old and 17 of them were female. Their main diagnoses were chronic renal failure in hemodialysis in 48%, uremic syndrome in 36% and renal transplant in 6%. Seventy nine percent had a history of antimicrobial use (42% quinolones and 36% cephalosporins). In 3 patients, the only risk factor was chronic renal failure. Seventy five percent responded to metronidazole and in 27%, diarrhea recidivated, compared with a 6% recurrence rate in other units, p < 0.02). Eight patients died during hospital stay. CONCLUSIONS Among patients with renal diseases, Clostridium difficile is frequent and associated with a high recurrence rate and mortality. Chronic renal failure may be a risk factor for its development.