Miracle-dz/UniFAR-FTUs huggingface dataset:
Emerging translation strategies during virus–host interaction

Translation control is crucial during virus–host interaction. On one hand, viruses completely rely on the protein synthesis machinery of host cells to propagate and have evolved various mechanisms to redirect the host's ribosomes toward their viral mRNAs. On the other hand, the host rewires its translation program in an attempt to contain and suppress the virus early on during infection; the antiviral program includes specific control on protein synthesis to translate several antiviral mRNAs involved in quenching the infection. As the infection progresses, host translation is in turn inhibited in order to limit viral propagation. We have learnt of very diverse strategies that both parties utilize to gain or retain control over the protein synthesis machinery. Yet novel strategies continue to be discovered, attesting for the importance of mRNA translation in virus–host interaction. This review focuses on recently described translation strategies employed by both hosts and viruses. These discoveries provide additional pieces in the understanding of the complex virus–host translation landscape.
What Ought a Program Committee to Do?

When the Internet was initially constructed it was a defacto playground for researchers. The research community built the Internet and refined it by monitoring traffic and tinkering with protocols and applications. The days of the Internet being a research sandbox are clearly over. Today, society at-large depends on the Internet as a crucial piece of infrastructure for communication and commerce. As such, experimenting with and monitoring today’s Internet is a much more thorny endeavor than in the past because researchers must consider the impact of their experiments on users. The community has started to face questions about the propriety of certain experiments and will no doubt continue to struggle with such issues going forward. In this note, we ponder the role of a program committee when faced with submissions that involve a potentially unacceptable experimental methodology. We note that the community already charges program committees with dealing with a number of ethical issues such as plagiarism, simultaneous submissions and conflicts of interest. Should dealing with questions about the ethics of a particular experimental methodology also be on the PC’s plate? Certainly we are aware of PCs that have taken it upon themselves to include such issues in the debate over particular submissions. Are such considerations “in bounds” for PC consideration? Or, should PCs stick to the technical aspects of submissions? To give the reader a concrete flavor of the sorts of questions that might arise during PC deliberations we sketch possible reactions to several recently published paper as examples.
The chromosomes of the Didelphidae (Marsupialia) and their evolutionary significance

One hundred and seventy-seven specimens of American didelphids, representing 9 genera and 22 species have been studied for their chromosomal constitution. Didelphids are very conservative in chromosomal complements. All of the studied species can be sorted into one of three kinds of karyotypes: 2n= 14 (three species of Didelphis, one of Lutreolina, two of Philander, and one of Chironectes), 2n = 14 (eight species of Marmosa, one of Metachirus, three of Caluromys, and one of Dromiciops), and 2n= 18 (three species of Monodelphis). These karyotypes are stable, showing only minor variations within each basic pattern. It is concluded that chromosomals evolution in the Didelphidae proceededs from low numbers to higher numbers by a process of centromeric fissioning complemented by some pericentric inversions and/or translocations. The pattern of karyotypic stability is consistent with bradytely at the organismic level of evolution. This is explained by a low rate of regulatory genetic evolution promoted by epistatic selection favouring the retention of chromosomal arrangements highly advantageous for overall adaptation.
A comparative analysis of the carbon intensity of biofuels caused by land use changes

Worldwide land is a limited resource and its use for the production of biofuels and other agricultural products can impact greenhouse gas emissions (GHG). Several models and approaches have been used to assess the direct (dLUC) and indirect land use change (iLUC) carbon intensity – i.e. the amount of CO2 emitted per unit of biofuel produced – of biofuels, but their outcomes diverge significantly. This analysis of 15 studies published between 2008 and 2010 (i) summarized and compared models and approaches used to estimate the dLUC and iLUC carbon intensities of biofuels, and (ii) assessed the mechanisms that led to the variation in the outcomes. The data show that the dLUC carbon intensity ranged from −52 to 34 g CO2 MJ−1, whereas the iLUC ranged from 0 to 327 g CO2 MJ−1 for bioethanol depending on the feedstock, on the type of land used or displaced and on the amortization period. The total LUC carbon intensity of bioethanol was found to be −29% to 384% of that of gasoline. This means that in some cases, LUC could potentially alter the GHG benefits of biofuels. Standardizing assumptions, carbon stock changes and methodologies for estimating the dLUC and iLUC carbon intensity will ensure more consistency and meaningful comparisons across studies in the future. This might then enable policy makers to make better justified judgments on the sustainability of biofuels.
Lightweight Centrality Measures in Networks under Attack

In this paper we study deliberate attacks on the infrastructure of large scale-free networks. These attacks are based on the importance of individual vertices in the network in order to be successful, and the concept of centrality (originating from social science) has already been utilized in their study with success. Some measures of centrality however, as betweenness, have disadvantages that do not facilitate the research in this area. We show that with the aid of scale-free network characteristics such as the clustering coefficient we can get results that balance the current centrality measures, but also gain insight into the workings of these networks.
Separating Components of Variation in Survival of Mule Deer in Colorado

Abstract Survival is an important parameter for understanding population dynamics of mule deer (Odocoileus hemionus) and other large herbivores. To understand long-term dynamics it is important to separate sampling and biological process variation in survival. Moreover, knowledge of correlations in survival across space and between young and adults can provide more informed predictions of survival in unsampled areas. We estimated survival of fawn, yearling, and adult mule deer from 4 spatially separated regions of Colorado, USA, from 1997 to 2008. We also estimated process variance in survival across time for each age and site using Markov chain Monte Carlo (MCMC) methods. Finally, we estimated correlations in survival among sites and ages with MCMC methods. Average winter fawn survival was 0.721 (SD = 0.024) for the 4 regions. Average winter adult female survival was 0.935 (SD = 0.007). Annual adult female survival ranged from 0.803 (SD = 0.017) to 0.900 (SD = 0.028) for the 4 regions, excluding hunting mortality. The correlation between fawn and adult female survival was high, 0.563 (SD = 0.253). Correlations in winter fawn survival were higher between populations at the same latitude than they were for populations to the north and south. We used survival estimates from our analysis to inform prior distributions for a Bayesian population dynamics model from one population in Colorado and compared that model to one with noninformative prior distributions. Population models including informative prior distributions based on our results performed better than those noninformative prior distributions on survival, providing more biologically defensible results when data were sparse. Knowledge of process distributions of survival can help wildlife managers better predict future population status and understand the likely range of survival rates.
Acidic polysaccharides from Psidium cattleianum (Araçá)

The aim of this work was to study the acidic polysaccharides of Psidium cattleianum. Pectic fractions were obtained by successive extractions with water, EDTA and sodium carbonate (4 and 25oC). Monosaccharide composition, total carbohydrates, uronic acids and protein contents were determined for each fraction. The yield of water and EDTA-soluble fractions and high content of uronic acid were consistent with the presence of pectins probably arising from the middle lamellae. On the other hand, sodium carbonate-soluble pectins had a higher neutral sugar content, indicating highly branched polysaccharides in these fractions, consistent with pectins from cell wall.
Task division and tracking based on macro-micro manipulators system for discontinuous trajectory

Ibis paper presents a kind of strategy of task division to process the discontinuous trajectory tracking. Using cubic spline with string parameter to fit the discontinuous trajectory result in: (a) the desired trajectory for macro manipulator is continuous, of which, the discontinuous parts will be tracked by the micro manipulator; and (b) macro-micro manipulator - the redundant system can be regarded as two non-redundant sub-systems. In trajectory planning, a computing algorithm for maximum velocity and maximum acceleration are given based upon trapezoidal velocity profile and torque constraints. Besides tracking the divided trajectory, micro manipulator compensates the trajectory errors caused by macro manipulator. Simulations and experiments of discontinuous trajectory tracking verify the effectiveness of our strategy.
Study of Cystatin C Level for Detection of Renal Dysfunction with Tenofovir Treatment in Human Immunodeficiency Virus Infection

12.00 Nowadays, an antiretroviral drug, tenofovir disoproxil fumarate (TDF), has been increasingly prescribed to HIV/AIDS patients. However, renal disorder or renal failure in some patients with risk factors has been presented. The standard glomerular filtration rate (GFR) test which is quite cumbersome and expensive has been requested. Various alternative tests have been evaluated but the results revealed some inconsistencies. Many studies indicated that serum cystatin C has high correlation with GFR result. This study aimed to investigate the cystatin C levels for monitoring renal dysfunction in TDF treated HIV patients. The prospective study was conducted on 171 patients comprising 3 different groups: HIV patients treated with tenofovir (TDF), HIV patients treated with other antiretroviral drugs (nonTDF) and anti-HIV negative group (control group). The levels of cystatin C, creatinine, and estimated glomerular filtration rate (eGFR) were monitored. The TDF group had a 9-fold higher risk of developing abnormal cystatin C levels than the control group ( OR 9.18, 95% CI 1.05 – 79.70) with statistically significant differences ( P 0.05). In addition, the cystatin C level in nonTDF group was also not significantly different from the control group ( P > 0.05). Owing to some limitations of this study, it cannot be definitely concluded that the testing of cystatin C levels can be a potential tool in diagnosing renal dysfunction in tenofovir-treated HIV patients. Normal 0 false false false EN-US X-NONE TH
Genetic, physiological and ecological diversity of the diatom genus Leptocylindrus

Diatoms are among the most productive photoautotrophic organisms on Earth. Within the diatom genus Leptocylindrus, two species, L. danicus and L. minimus, are reported as abundant in coastal waters worldwide and in the Gulf of Naples (GoN). This thesis aimed at a closer characterisation of Leptocylindrus species through different approaches, including the study of their morphology, molecular phylogeny, metagenomics and biochemistry. Eighty-three strains from the GoN and one strain (CCMP 1856) from the Atlantic US coast were analysed. Based on the morphological, molecular and life cycle differences, the taxonomy of the genus was revised. The GoN species previously identified as L. minimus was in fact identified as L. belgicus Meunier and was placed in a new genus, Tenuicylindrus Nanjappa and Zingone which, along with Leptocylindrus Cleve, belongs to the family Leptocylindraceae. Five species in all were included in the genus Leptocylindrus: L. danicus Cleve and L. minimus Gran, two novel species L. hargravesii and L. convexus, and L. aporus (Hargraves) Nanjappa & Zingone, which was raised from the variety to the species status. The real Leptocylindrus minimus was not found in the GoN. To address the distribution of the 6 species outside the GoN, two metagenomic databases, BioMarKs (Europe) and Tara Oceans (worldwide) were explored. Sequences of L. aporus, L. convexus and L. danicus were recovered at many sites in European waters and across the world's seas, while those of L. minimus were retrieved only in the Oslo fjord and those of T. belgicus were only found in the GoN and Oslo fjord. Additional diversity was observed in the Tara Oceans dataset but, in lack of morphological information, whether this diversity is real remains to be clarified. All species except L. minimus were also categorised based on the diversity in their oxylipins pathways. Leptocylindrus danicus and L. hargravesii shared common lipoxygenase pathways, different from the ones shared by the species L. aporus and L. convexus. Tenuicylindrus belgicus exhibits a pathway distinct from that of Leptocylindrus species. Species-specific compounds produced in minor quantities were also observed. Physiological experiments show that L. aporus can withstand higher (26 "C) temperature but not lower (12 CC) temperature, while L. danicus can withstand low temperature but not high temperature. This corresponds to the species occurrence in the natural environment, where L. aporus blooms during summer and L. danicus is found in all seasons except summer. Altogether, through an interdisciplinary approach, the studies described in this thesis provide substantial information that may have important implications in the field of ecology, evolution, conservation biology and biotechnology.
Why stabilise? Using triaxial tests for determining pavement stiffness and shear strength parameters of mechanically modified layers

Triaxial testing of naturally occurring, slightly silty, medium-graded, coarse sand, derived from completely weathered granite (with some gypsum), compacted to 95 % of Mod AASHTO density generated unload / reload Young's modulus E-values of about 300 MPa at a representative confining stress of 90 kPa. This is some 80 % higher than what would usually be expected for this type of G5 material. Mohr-Coulomb shear strength parameters of c = 15,9 kPa and φ = 51,4o were obtained from the high-quality triaxial tests. Taking into account the variability of the materials, it is suggested that these be downgraded to c = 12,7 kPa and φ = 48,8o for use as design parameters. It is common practice to stabilise natural gravel materials to generate weakly cemented sub-base layers. However, the presence of naturally occurring gypsum within the in-situ granite generated concern as negative effects were observed on elements of past construction. The use of cement as a stabilising agent was eliminated by generating a nearly equally strong layer by mixing the naturally occurring gravels with varying quantities of crushed stone, crusher waste and dune sand, the latter to combat a high plasticity index. The best result was obtained by using a blend of 50 % natural gravel, 30 % crusher waste and 20 % dune sand. These blended materials, generated unload / reload Young's modulus E-values of some 560 MPa at 95 % Mod AASHTO compaction and a confining stress of 247 kPa. This E-value is very similar to what is thought would be attained for a cracked and hydrated cement-stabilised layer but without the disruptive effects of a lowered confining stress that would be the case when a stabilised layer shrunk and cracked on hydration of the cement stabilising agent.
Comparative analysis of morphological characteristics and effective composition content of wild and cultivated Epimedium pubescens and Epimedium wushanense (Berberidaceae)

The effective composition content were determined in Cultivated and wild of Epimedium pubescens and Epimedium wushanense by High-Pressure Liquid Chromatography (HPLC) and ultraviolet-visible (UV), and the difference of morphological parameters and effective composition content were analyzed by one-way ANOVA statistical analysis. The results showed that because of the relative light intensity increased, the dwarf phenomenon was occurred in Cultivated E. pubescens and E. wushanense, but the number of branches and leaf number per plant in cultivated were more than wild, and increased the output of two kinds of Epimedium. According to the standard of Chinese Pharmacopoeia, both wild and cultivated leaves the icariin contents of E. pubescens can meet the standard. Insignificant difference in flavonoid contents between the cultivated and wild leaves of E. wushanense, but both can meet the standard, both wild and cultivated all other parts of E. wushanense cannot meet the standard of icariin contents, which may be related to harvesting time. Key words: Epimedium pubescens, Epimedium wushanense, wild and cultivated, effective composition, morphological characteristics.
A comparative study of optimization methods and conventional methods for sampling design in fishery-independent surveys

Liu, Y. , Chen, Y. , and Cheng, J. 2009. A comparative study of optimization methods and conventional methods for sampling design in fishery-independent surveys. - ICES Journal of Marine Science, 66: 1873-1882.We have introduced and evaluated a procedure, the constrained spatial simulated annealing method, for developing an optimal sampling design for fishery-independent surveys. We used two criterion functions, minimization of the mean of the shortest distance (MMSD) and uniform distribution of point pairs for variogram estimation (WM), and three arrangements of the two criteria, all WM, all MMSD, and a combination of MMSD (2/3 of samples) and WM (1/3), to construct three optimized sampling designs (denoted as Designs I, II, and III, respectively). These three designs were compared in a simulation study with systematic sampling (Design IV) and stratified random sampling designs (Design V), commonly used in fishery-independent surveys. Three levels of sample size (small, medium, and large) were considered in the simulation study developed using a geostatistical approach. The results showed that for parameter estimation of the spatial covariance function, Design III was better than the other designs at relatively small sample size and Design II performed better than the other designs at relatively large sample size. For estimating fish stock abundance, the performance of the designs considered in this study can be ranked as follows: Design II > Design IV > Design III > Design V > Design I. It is clearly important to evaluate and improve sampling design based on historical survey data. Such a study allows us to identify an optimal sampling design to balance the quality of the data collected and the costs of the sampling programme, leading to the development and optimization of a sustainable and fishery-independent monitoring programme.
Phenolic compounds in virgin olive oils : Fractionation by solid phase extraction and antioxidant activity assessment

The polar fraction of virgin olive oil was separated into two main parts (A and B) using solid phase extraction. Analysis of individual components by RP-HPLC indicated that the part (A) contained only simple phenols and phenolic acids. Part (B) had a complex nature. The two parts tested for their antioxidant activity showed relatively high protection factors in safflower oil stored at 80°C. Part B was found to contribute more than part A to the stability of the oil. The antioxidant activity of both fractions was related to their content of total polyphenols and o-diphenols. Acidic and alkaline hydrolysis showed significant quantitative changes in the HPLC profiles indicating the presence of ether and ester bonds while high-performance anion exchange chromatography of sugars after hydrolysis gave evidence for the presence of only traces of glycosides. A first attempt to identify a characteristic chromatographic peak of part B by HPLC fractionation and mass spectrometry showed the presence of an ester of tyrosol most probably with a dicarboxylic acid. © 1997 SCI.
Help-seeking by male victims of domestic violence and abuse (DVA): a systematic review and qualitative evidence synthesis

Objectives To understand help-seeking by male victims of domestic violence and abuse (DVA) and their experiences of support services by systematically identifying qualitative and mixed-method studies and thematically synthesising their findings. Design Systematic review and qualitative evidence synthesis. Searches were conducted in 12 databases and the grey literature with no language or date restrictions. Quality appraisal of the studies was carried out using the Critical Appraisal Skills Programme tool. Reviewers extracted first and second order constructs related to help-seeking, identified themes and combined them by interpretative thematic synthesis. Setting DVA experienced by male victims and defined as any incident or pattern of incidents of controlling coercive or threatening behaviour, violence or abuse among people aged 18 or over who are or have been intimate partners or family members, regardless of gender or sexuality. Participants Male victims of DVA. Interventions Any intervention which provides practical and/or psychological support to male victims of DVA including but not limited to DVA-specific services, primary healthcare and sexual health clinics. Primary and secondary outcome measures Qualitative data describing help-seeking experiences and interactions with support services of male victims of domestic violence Results We included twelve studies which were published between 2006 and 2017. We grouped nine themes described over two phases (a) barriers to help-seeking: fear of disclosure, challenge to masculinity, commitment to relationship, diminished confidence/despondency and invisibility/perception of services; and (b) experiences of interventions and support: initial contact, confidentiality, appropriate professional approaches and inappropriate professional approaches. Conclusion The recent publication of the primary studies suggests a new interest in the needs of male DVA victims. We have confirmed previously identified barriers to help-seeking by male victims of DVA and provide new insight into barriers and facilitators to service provision. PROSPERO registration number CRD42016039999.
The biology of Canadian weeds. 129. Phragmites australis (Cav.) Trin. ex Steud.

Phragmites australis (Cav.) Trin. ex Steud. -common reed, is a perennial, emergent aquatic plant with annual cane-like stems developed from an extensive rhizome system. It grows in low-lying wet areas such as fresh and salt-water marshes, drainage ditches, shallow lake edges, sandy banks, roadsides, woodlands and rocky places. Stems can reach up to 6.0 m in height, vary in diameter from 4 to10 mm and have 10 to 25 cm long hollow internodes. Clones are extended by perennial rhizomes with extensive aerenchymatous tissue that supplies oxygen. Roots develop from rhizomes and other submerged parts of shoots. Leaves are smooth, alternate with narrow-lanceolate laminae, 20 to 70 cm long and 1 to 5 cm broad, and tapering to long slender points. The inflorescence is a terminal panicle, often 30 cm long, dull purple to yellow, with main branches bearing many spikelets. Seed production and germination are extremely variable and comparatively rare in many populations. Phragmites australis carries out photosynthesis th.