Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Regulation of Distinct Internal Ribosome Entry Sites of the Dicistroviridae Cricket Paralysis Virus

Internal ribosome entry is a key mechanism for viral protein synthesis in a subset of RNA viruses. Cricket paralysis virus (CrPV), a member of Dicistroviridae, has a positive-sense single strand RNA genome that contains two internal ribosome entry sites (IRES), a 5′untranslated region (5′UTR) and intergenic region (IGR) IRES, that direct translation of open reading frames (ORF) encoding the viral non-structural and structural proteins, respectively. The regulation of and the significance of the CrPV IRESs during infection are not fully understood. In this study, using a series of biochemical assays including radioactive-pulse labelling, reporter RNA assays and ribosome profiling, we demonstrate that while 5′UTR IRES translational activity is constant throughout infection, IGR IRES translation is delayed and then stimulated two to three hours post infection. The delay in IGR IRES translation is not affected by inhibiting global translation prematurely via treatment with Pateamine A. Using a CrPV replicon that uncouples viral translation and replication, we show that the increase in IGR IRES translation is dependent on expression of non-structural proteins and is greatly stimulated when replication is active. Temporal regulation by distinct IRESs within the CrPV genome is an effective viral strategy to ensure optimal timing and expression of viral proteins to facilitate infection.
Illusion Master: Extending Self-Presence and Challenging Immersion in and through Digital Games

This paper provides an extension of the definition of the concept of selfpresence (named Objective self-presence) in digital games, and in doing so, challenges the traditional concepts of immersion and presence / self-presence in games. The design process of the submitted game Illusion Master is used as a case study to show how the related concepts of presence and immersion can be addressed in a different manner in and through digital games. It is argued that self-presence need not necessarily involve a situation where players feel as if their virtual self is their actual self. In games studies, this definition of presence is very much linked to the concept of immersion, which looks at how a player is surrounded by an immersive new reality. In this paper, it is argued that selfpresence can also manifest itself through a double-consciousness where a player is both engrossed in the game, while remaining conscious of him/herself as a human being engaging with a game outside the game world.
Towards a Reliable Spam-Proof Tagging System

Tagging systems are particularly vulnerable to tag spam. Although some previous efforts aim to address this problem with detection-based or demotion-based approaches, tricky attacks launched by attackers who can exploit vulnerabilities of spam-resistant mechanisms are still able to invalidate those efforts. Therefore, it is challenging to resist tricky spam attacks in tagging systems. This paper proposes a novel spam-proof tagging system, which can provide high-quality tag search results even under tricky attacks, based on four key insights: demotion-based strategy, reputation, altruistic users and social networking. Specifically, our system upgrades/degrades the ranks of correct/incorrect content items in search results through introducing personalized users' reliability degrees and responsible users, thus avoiding clients pick unwanted content. Experimental results illustrated our system could effectively defend against tricky tag spam attacks and work better than current prevalent tag search models.
New protein–protein interactions of mitochondrial connexin 43 in mouse heart

Connexin 43 (Cx43), the gap junction protein involved in cell‐to‐cell coupling in the heart, is also present in the subsarcolemmal fraction of cardiomyocyte mitochondria. It has been described to regulate mitochondrial potassium influx and respiration and to be important for ischaemic preconditioning protection, although the molecular effectors involved are not fully characterized. In this study, we looked for potential partners of mitochondrial Cx43 in an attempt to identify new molecular pathways for cardioprotection. Mass spectrometry analysis of native immunoprecipitated mitochondrial extracts showed that Cx43 interacts with several proteins related with mitochondrial function and metabolism. Among them, we selected for further analysis only those present in the subsarcolemmal mitochondrial fraction and known to be related with the respiratory chain. Apoptosis‐inducing factor (AIF) and the beta‐subunit of the electron‐transfer protein (ETFB), two proteins unrelated to date with Cx43, fulfilled these conditions, and their interaction with Cx43 was proven by direct and reverse co‐immunoprecipitation. Furthermore, a previously unknown molecular interaction between AIF and ETFB was established, and protein content and sub‐cellular localization appeared to be independent from the presence of Cx43. Our results identify new protein–protein interactions between AIF‐Cx43, ETFB‐Cx43 and AIF‐ETFB as possible players in the regulation of the mitochondrial redox state.
A K-band central disc surface brightness correlation with scalelength for early-type disc galaxies, and the inclination correction

The K-band light profiles from two statistically complete, diameter-limited samples of disc galaxies have been simultaneously modelled with a seeing-convolved Sersic r1/n bulge and a seeing-convolved exponential disc. This has enabled an accurate separation of the bulge and disc light, and hence an estimate of the central disc surface brightness μ0,K and the disc scalelength h. There exists a bright envelope of galaxy discs in the μ0,K–log h diagram; for the early-type (≤Sbc–Sc) disc galaxies μ0,K is shown to increase with log h, with a slope of ∼2 and a correlation coefficient equal to 0.75. This relation exists over a range of disc scalelengths from 0.5 to 10 kpc (H0=75 km s−1 Mpc−1). In general, galaxy types Scd or later are observed to deviate from this relation; they have fainter surface brightnesses for a given scalelength. With a subsample of 59 low-inclination (i≤50°) and 29 high-inclination (i≥50°) galaxies having morphological types ranging from S0 to Sc, the need for an inclination correction to the K-band disc surface brightness is demonstrated. Certain selection criteria biases which have troubled previous surface brightness inclination tests (for example, whether the galaxies are selected from a magnitude- or diameter-limited sample) do not operate in the μ0,K–log h diagram. Measured central disc surface brightnesses are found to be significantly (>5σ) brighter for the high-inclination disc galaxies than for the low-inclination disc galaxies. With no surface brightness inclination correction or allowance for the trend between μ0,K and log h, the standard deviation to the distribution of μ0,K values is ∼1 mag arcsec−2, while the standard deviation about the mean μ0,K–log h relation decreases from 0.69 mag arcsec−2, when no inclination correction is applied, to 0.47 mag arcsec−2 when the inclination correction is applied. Possible changes to the disc scalelength with inclination, as a result of radial gradients in the disc opacity, have been explored. The maximum possible sizes for such corrections are too small to provide a valid explanation for the difference between the low- and high-inclination disc galaxies in the μ0,K–log h diagram.
Ambulatory arterial stiffness index, pulse wave velocity and augmentation index – interchangeable or mutually exclusive measures?

Background The ambulatory arterial stiffness index (AASI) has been proposed as a novel measure of arterial stiffness and has been prospectively shown to predict stroke and cardiovascular death, but not cardiac death. This index has prompted considerable controversy as to whether it is a true measure of arterial stiffness. Objective and methods The present study aimed to examine three different measures of arterial stiffness – pulse wave velocity (PWV; Complior), wave reflection [augmentation index (AIx)] and AASI – in a large hypertensive population, comparing their determinants and intercorrelations, both unadjusted and adjusted for confounders, and using Bland–Altman analysis to determine 95% confidence intervals for the ability of the AASI to predict PWV, the proposed gold standard of arterial stiffness. Results The AASI correlated univariately with both PWV and the AIx in individuals overall (r = 0.28 for PWV and r = 0.24 for AIx; both P < 0.001) and in those with untreated or treated hypertension. Adjustment for age in the current study negated entirely the positive correlation between the AASI, PWV and AIx. Additional adjustment for confounders did not significantly alter these nonsignificant relationships. Furthermore, the 95% prediction limits for the AASI to predict PWV were ± 4.18 m/s and for the AASI to predict AIx were ± 25.4%, suggesting that the methods would not be interchangeable in a clinical setting. Direct comparative studies would be required to establish the relative predictive strength of each measure and whether combining measures can provide additional risk prediction. Until such data become available, we propose that the measures should not be considered interchangeable.
Correlates of postnatal depression among women in Zimbabwean semi-urban and rural settings

This study explored antecedents to postnatal depression and its prevalence in semi-urban and rural Zimbabwean communities. 115 women completed the Edinburgh Postnatal Depression Scale. The mean age of participants was 25.8 years (SD = 5.4 years). Descriptive statistical analysis indicated a postnatal depression prevalence of 30.5%. Factors associated with postpartum depression were: intimate partner violence (p = 0.02), history of childhood abuse (p < 0.001), lack of social support (p < 0.01) and having a female child as the first child (p = 0.004). Prevalence for postnatal depression is high in this setting and it is imperative to identify women at risk of depression through screening so that psychological interventions can be instituted in primary care settings.
Weblogs as a bridging genre

Purpose – Aims to describe systematically the characteristics of weblogs (blogs) – frequently modified web pages in which dated entries are listed in reverse chronological sequence and which are the latest genre of internet communication to attain widespread popularity.Design/methodology/approach – This paper presents the results of a quantitative content analysis of 203 randomly selected blogs, comparing the empirically observable features of the corpus with popular claims about the nature of blogs, and finding them to differ in a number of respects.Findings – Notably, blog authors, journalists and scholars alike exaggerate the extent to which blogs are interlinked, interactive, and oriented towards external events, and underestimate the importance of blogs as individualistic, intimate forms of self‐expression.Originality/value – Based on the profile generated by the empirical analysis, considers the likely antecedents of the blog genre, situates it with respect to the dominant forms of digital communica.
Methods for Evaluating Fly Ash for Use in Highway Concrete

This report presents recommended changes to coal fly ash specifications and test protocols contained in AASHTO Standard Specifications for Transportation Materials and Methods of Sampling and Testing (AASHTO M 295). These changes include modifications to the test methods currently specified for evaluating acceptability of fly ash for use in highway concrete as well as the introduction of new test methods for enhancing such evaluations. The modified specifications and test protocols will guide materials engineers and fly ash producers in evaluating fly ash and assuring that highway concrete is enhanced, and not deleteriously affected, by replacing a portion of the cement in the concrete mixture with fly ash. The information contained in the report will be of immediate interest to state materials engineers and others involved in specifying and evaluating concrete mixtures for use in highway pavements and structures.
OD practitioner values and the impact on environmental behavior

Organization Development has the potential to play an active role in supporting environmental change initiatives. This study explores the values of a group of OD practitioners who are working with environmental concerns as a consideration in their practice. Nine qualitative interviews were conducted to explore values and surface factors that have influenced those values. The Schwartz Value Questionnaire (SVQ) and the Nature Relatedness Scale were administered to better understand practitioner values. Elements of self-transcendent values were revealed amongst practitioners through both quantitative and qualitative methods. In addition, these practitioners scored higher than the average population on Nature Relatedness. This study supported research, which linked an individual’s self-transcendent values to feelings of environmental concern. This study also supported research by Schein (2014), which showed that certain experiences shaped ecological worldviews of sustainability leaders over their lifespan. OD has an opportunity to enable more of its students and practitioners to adopt this ecological worldview and gravitate towards leveraging OD expertise in the environmental sustainability space.
Agglomeration and the Adjustment of the Spatial Economy

We consider the literatures on urban systems and New Economic Geography to examine questions concerning agglomeration and how areas respond to shocks to the economic environment. We first propose a diagrammatic framework to compare the two approaches. We then use this framework to study a number of extensions and to consider several policy relevant issues.
Role of Macrophages in the Repair Process during the Tissue Migrating and Resident Helminth Infections

The Th1/Th2/Th17 balance is a fundamental feature in the regulation of the inflammatory microenvironment during helminth infections, and an imbalance in this paradigm greatly contributes to inflammatory disorders. In some cases of helminthiasis, an initial Th1 response could occur during the early phases of infection (acute), followed by a Th2 response that prevails in chronic infections. During the late phase of infection, alternatively activated macrophages (AAMs) are important to counteract the inflammation caused by the Th1/Th17 response and larval migration, limiting damage and repairing the tissue affected. Macrophages are the archetype of phagocytic cells, with the primary role of pathogen destruction and antigen presentation. Nevertheless, other subtypes of macrophages have been described with important roles in tissue repair and immune regulation. These types of macrophages challenge the classical view of macrophages activated by an inflammatory response. The role of these subtypes of macrophages during helminthiasis is a controversial topic in immunoparasitology. Here, we analyze some of the studies regarding the role of AAMs in tissue repair during the tissue migration of helminths.
Gene expression profiling of NB4 cells following knockdown of nucleostemin using DNA microarrays

Nucleostemin (NS) is mainly expressed in stem and tumor cells, and is necessary for the maintenance of their self-renewal and proliferation. Originally, NS was thought to exert its effects through inhibiting p53, while recent studies have revealed that NS is also able to function independently of p53. The present study performed a gene expression profiling analysis of p53-mutant NB4 leukeima cells following knockdown of NS in order to elucidate the p53-independent NS pathway. NS expression was silenced using lentivirus-mediated RNA interference technology, and gene expression profiling of NB4 cells was performed by DNA microarray analysis. A total of 1,953 genes were identified to be differentially expressed (fold change ≥2 or ≤0.5) following knockdown of NS expression. Furthermore, reverse-transcription quantitative polymerase chain reaction analysis was used to detect the expression of certain candidate genes, and the results were in agreement with the micaroarray data. Pathway analysis indicated that aberrant genes were enhanced in endoplasmic, c-Jun N-terminal kinase and mineral absorption pathways. The present study shed light on the mechanisms of the p54-independent NS pathway in NB4 cells and provided a foundation for the discovery of promising targets for the treatment of p53-mutant leukemia.
Improved Limits on B0 Decays to Invisible Final States and to ννˉγ

We establish improved upper limits on branching fractions for B0 decays to final States 10 where the decay products are purely invisible (i.e., no observable final state particles) and for final states where the only visible product is a photon. Within the Standard Model, these decays have branching fractions that are below the current experimental sensitivity, but various models of physics beyond the Standard Model predict significant contributions for these channels. Using 471 million BB pairs collected at the Y(4S) resonance by the BABAR experiment at the PEP-II e+e- storage ring at the SLAC National Accelerator Laboratory, we establish upper limits at the 90% confidence level of 2.4x10^-5 for the branching fraction of B0-->Invisible and 1.7x10^-5 for the branching fraction of B0-->Invisible+gamma
Interspecific genetics of speciation phenotypes: song and preference coevolution in Hawaiian crickets

Understanding the genetic architecture of traits involved in premating isolation between recently diverged lineages can provide valuable insight regarding the mode and tempo of speciation. The repeated coevolution of male courtship song and female preference across the species radiation of Laupala crickets presents an unusual opportunity to compare the genetic basis of divergence across independent evolutionary histories. Previous studies of one pair of species revealed a polygenic basis (including a significant X chromosome contribution) to quantitative differences in male song and female acoustic preference. Here, we studied interspecific crosses between two phenotypically less‐diverged species that represents a phylogenetically independent occurrence of intersexual signalling evolution. We found patterns consistent with an additive polygenic basis to differentiation in both song and preference (nE = 5.3 and 5.1 genetic factors, respectively), and estimate a moderate contribution of the X chromosome (7.6%) of similar magnitude to that observed for Laupala species with nearly twice the phenotypic divergence. Together, these findings suggest a similar genetic architecture underlying the repeated evolution of sexual characters in this genus and provide a counterexample to prevailing theory predicting an association between early lineage divergence and sex‐linked ‘major genes’.
Osmoregulation of Lampetra fluviatilis L. and Petromyzon marinus (Cyclostomata) in hyperosmotic solutions.

1. Freshly caught migrating lampreys were placed in 50% sea water and their method of osmoregulation was analysed. Some osmoregulated more successfully than others. 2. Water balance is maintained by a mechanism involving the drinking of large quantities of water (up to 99.5 ml/kg/day). Sodium, potassium and chloride are absorbed by the intestine (often against a concentration gradient) with the subsequent uptake of water. Divalent ions are not readily absorbed by the intestine and there is some evidence for the secretion of magnesium and sulphate into the gut lumen. 3. The limited urine flow (up to 6.2 ml/kg/day) is used for the excretion of calcium, magnesium and sulphate in high concentrations, but the urine is never hyperosmotic to the blood. The urinary excretion of monovalent ions is not sufficient to eliminate those entering by the intestine and extrarenal excretion at the gills must presumably occur. 4. The breakdown of this osmoregulatory mechanism during the anadromous migration involves: an increase in the permeability of the integument to water, breakdown of the swallowing mechanism which is not dependent upon the occlusion of the alimentary canal, a reduction in the ability to absorb monovalent ions and water from the ingested 50% sea water, and a loss in the large mitochondria-rich ‘chloride output cells’ of the gills. 5. The similarities between the mechanisms of ‘marine’ osmoregulation of lampreys and teleosts are discussed in terms of the evolution of the two groups, and it is concluded that almost identical osmoregulatory mechanisms have evolved independently.
Local estimation of posterior class probabilities to minimize classification errors

Decision theory shows that the optimal decision is a function of the posterior class probabilities. More specifically, in binary classification, the optimal decision is based on the comparison of the posterior probabilities with some threshold. Therefore, the most accurate estimates of the posterior probabilities are required near these decision thresholds. This paper discusses the design of objective functions that provide more accurate estimates of the probability values, taking into account the characteristics of each decision problem. We propose learning algorithms based on the stochastic gradient minimization of these loss functions. We show that the performance of the classifier is improved when these algorithms behave like sample selectors: samples near the decision boundary are the most relevant during learning.
Identification of a Novel Fungus, Leptosphaerulina chartarum SJTU59 and Characterization of Its Xylanolytic Enzymes

Xylanolytic enzymes are widely used in processing industries, e.g., pulp and paper, food, livestock feeds, and textile. Furthermore, certain xylanotic enzymes have demonstrated the capability to improve the resistance and immunity of plants. Screening of high-yield microbial xylanolytic enzyme producers is significant for improving large-scale cost-effective xylanolytic enzyme production. This study provided new evidence of high-level xylanolytic enzyme production by a novel fungus, designated Leptosphaerulina chartarum SJTU59. Under laboratory conditions, L. chartarum SJTU59 produced xylanolytic enzymes of up to 17.566 U/mL (i.e., 878.307 U/g substrate). The enzyme solution was relatively stable over a wide range of pH (pH 3.0 to pH 9.0) and temperature (40°C to 65°C) while showing high resistance to the majority of metal ions tested. Composition analysis of the hydrolytic products of xylan showed sufficient degradation by xylanolytic enzymes from L. chartarum SJTU59, mainly the monosaccharide xylose, and a small amount of xylobiose were enzymatically produced; whereas in the presence of sufficient xylan substrates, mainly xylooligosaccharides, an emerging prebiotic used in food industry, were produced. In addition, the xylanolytic enzyme preparation from L. chartarum SJTU59 could initiate tissue necrosis and oxidative burst in tobacco leaves, which may be related to enhanced plant defense to adversity and disease. L. chartarum SJTU59 possessed a complex xylanolytic enzyme system, from which two novel endo-β-1,4-xylanases of the glycoside hydrolase (GH) family 10, one novel endo-β-1,4-xylanase of the GH family 11, and one novel β-xylosidase of the GH family 43 were obtained via rapid amplification of complementary DNA ends. Given the high yield and stable properties of xylanolytic enzymes produced by L. chartarum SJTU59, future studies will be conducted to characterize the properties of individual xylanolytic enzymes from L. chartarum SJTU59. xylanolytic enzymes-encoding gene(s) of potential use for industrial and agricultural applications will be screened to construct genetically engineered strains.