Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A. thaliana is 6.95 × 10−9 (SE ± 2.68 × 10−10) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10−9 (±1.07 × 10−10) per site per generation, with deletions being more frequent and larger than insertions. Among the 1694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that de novo mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.
Combined effects of CO2 and temperature on carbon uptake and partitioning by the marine diatoms Thalassiosira weissflogii and Dactyliosolen fragilissimus

Carbon uptake and partitioning of two globally abundant diatom species, Thalassiosira weissflogii and Dactyliosolen fragilissimus, was investigated in batch culture experiments under four conditions: ambient (15°C, 400 μatm), high CO2 (15°C, 1000 μatm), high temperature (20°C, 400 μatm), and combined (20°C, 1000 μatm). The experiments were run from exponential growth into the stationary phase (six days after nitrogen depletion), allowing us to track biogeochemical dynamics analogous to bloom situations in the ocean. Elevated CO2 had a fertilizing effect and enhanced uptake of dissolved inorganic carbon (DIC) by about 8% for T. weissflogii and by up to 39% for D. fragilissimus. This was also reflected in higher cell numbers, build‐up of particulate and dissolved organic matter, and transparent exopolymer particles. The CO2 effects were most prominent in the stationary phase when nitrogen was depleted and CO2(aq) concentrations were low. This indicates that diatoms in the high CO2 treatments could take up more DIC until CO2 concentrations in seawater became so low that carbon limitation occurs. These results suggest that, contrary to common assumptions, diatoms could be highly sensitive to ongoing changes in oceanic carbonate chemistry, particularly under nutrient limitation. Warming from 15 to 20 °C had a stimulating effect on one species but acted as a stressor on the other species, highlighting the importance of species‐specific physiological optima and temperature ranges in the response to ocean warming. Overall, these sensitivities to CO2 and temperature could have profound impacts on diatoms blooms and the biological pump.
Evolutionary history of the seagrass genus Posidonia

Seagrasses are the structural species of one of the most important coastal ecosystems worldwide and support high levels of biodiversity and biomass production. Posidonia is one of the most ancient seagrass genera and displays a contrasting disjunct biogeographic pattern. It contains one single species in the Northern Hemisphere, P. oceanica, which is endemic to the Mediterranean Sea, and has up to 8 recognized taxa in the Southern Hemisphere, which in Australia are divided into 2 complexes, P. ostenfeldii and P. australis. A phylogeny based on a nuclear marker (rRNA-ITS) revealed an ancient split between the northern (i.e. Mediterranean) and southern (i.e. Australian) taxa, followed by a separation of the 2 recognized Australian complexes. However, the species belonging to the P. ostenfeldii complex were indistinguishable, suggesting an ecotypic origin or a recent speciation. Therefore, among the 7 morphologically described Australian species only 4 spe- cies lineages can be discriminated. The organelle markers nad7 intron, trnL-F and mat K/trnK intron were not informative for reconstructing the phylogeny of this genus, and the mitochondrial markers exhibited a strikingly slow evolutionary rate relative to other genome regions.
FIB-4 and APRI scores for predicting severe fibrosis in chronic hepatitis C - a developing country's perspective in DAA era.

INTRODUCTION Chronic Hepatitis C Virus (HCV) infection leads to progressive fibrosis making fibrosis staging necessary in the evaluation of such patients. Different fibrosis scores are emerging as possible non-invasive alternatives for liver biopsy. The Fibrosis-4 Index (FIB-4) and AST to Platelet Ratio Index (APRI) scores are the most widely used and the most extensively tested. This study aims to determine if it was possible to accurately use these to identify patients that are unlikely to have severe fibrosis. METHODOLOGY One hundred and forty-two patients with chronic hepatitis C infection who underwent liver biopsy since January 1st 2014 until May 31st 2017 at the Hospital for Infectious and Tropical Diseases in Belgrade were analyzed. The FIB-4 and APRI scores were calculated for each patient and compared to histologically determined fibrosis stage. RESULTS A comprehensive statistical analysis was conducted in order to compare patients with and without severe fibrosis and to evaluate the accuracy of the fibrosis scores. Patients with non-severe fibrosis were younger, had higher platelet counts and lower transaminase levels. FIB-4 had an AUC of 0.875 and the APRI score had an AUC of 0.861. No patients with severe fibrosis or cirrhosis had a FIB-4 lower than 1.08. FIB-4 was superior to APRI in identifying patients with severe fibrosis in the study cohort. CONCLUSION FIB-4 was superior to APRI in the recognition of severe fibrosis. FIB-4 may prove very useful in identifying patients without advanced liver disease, especially if other non-invasive methods are inaccessible.
THE WORLD BANK AND THE IMF MODELS OF STABILISATION AND ADJUSTMENT: ARE THEY COMPATIBLE?

The 1980s witnessed a significant increase in the importance and influence of the World Bank (WB) and the International Monetary Fund (IMF) on macroeconomic policy formulation and implementation in many Developing Countries. The dominance of the IMF and WB models on practical macroeconomic policy formulation and implementation, the fact that the models adopted by each one of those institutions differ significantly, and the distressing experience of conflicting strategies, priorities and conditionality, have encouraged research to develop a unique model which simultaneously achieve the objectives of the two institutions and of the countries concerned. Researchers are beginning to ask whether the models are compatible, a third model (combining the two) is consistent, and if theoretical and methodological development along the lines and restrictive assumptions of the two models is worthy at all. This essay briefly discusses some of the literature analysing those questions. To do so, the essay is developed in six more sections. The first summarises the fundamental macroeconomic framework needed to analyse (im)balances and policy formulation. The second discusses the demand and the supply side types of adjustment and stabilisation programmes, as an
Inequality of opportunity in Europe: Economic and policy facts

In this paper we consider the main factors that have influenced inequality of opportunity (IO) in Europe. Based on the EU-SILC database, we find that the various levels of development, education and social protection expenditure in 23 European countries significantly affect IO. Dropping out from school, reaching at least secondary levels of education, social spending to promote social integration and child care are the most important variables of those analyzed. The functioning of the labor market and the tax structure, on the other hand, do not have a significant bearing on IO. Lastly, we note that IO and total inequality exhibit differentiated explanatory patterns, which signifies that means of redistribution that serve to reduce overall inequality do not necessarily reduce IO.
Clinical translation of autologous Schwann cell transplantation for the treatment of spinal cord injury

Purpose of reviewTo describe the current status of testing Schwann cell transplantation as a therapy for human spinal cord injury (SCI). Recent findingsTransplanted Schwann cells have reparative effects in the damaged spinal cord. A few clinical studies have reported that Schwann cell transplantation appears safe. Compared with allogeneic cell transplants, autologous cells do not require immune suppression, but the workload of cell manufacturing is greater. Preclinical Schwann cell transplant studies conducted at the University of Miami in 2009–2012 supported an investigational new drug approved by the Food and Drug Administration. A Phase 1 safety study has been initiated. SummarySpinal cord repair after severe SCI requires that axonal regeneration and myelination occur in a context of reduced inhibition, enhanced plasticity, and new circuit formation. Evolving clinical experience with Schwann cell transplantation may provide a basis upon which additionally combined therapeutics can be tested to increase the extent of repair after SCI. Safety is the primary consideration when ex-vivo manipulated cells are introduced into the damaged nervous system. Preclinical studies across several species have not indicated safety concerns regarding Schwann cells. Initial clinical reports from studies in Iran and China are suggestive of clinical safety, although more rigorous characterization of the implanted cells is needed.
Determination of 3D flame surface density variables from 2D measurements: Validation using direct numerical simulation

Three-dimensional compressible direct numerical simulation (DNS) data of freely propagating statistically planar turbulent premixed flames have been used to assess the accuracy of the isotropy- derived correction factors, which relate the two-dimensional projections of the different terms of the Reynolds averaged flame-surface density (FSD) transport equation with their corresponding actual three-dimensional counterparts for different values of Karlovitz number Ka, Lewis number Le, heat release parameter τ, and turbulent Reynolds number Ret. It is shown that the isotropic distribution of the surface area weighted probability density function (pdf) of the angle φ between the normal vectors on the measurement plane and on the flame surface provides a simple algebraic relation between the generalised FSDs evaluated in two and three dimensions (i.e., Σ2D and Σ3D), irrespective of the values of Ka,τ,Le, and Ret. Isotropic relations between two-dimensional and three-dimensional counterparts of the surface-avera.
Molecular dissection of multiphase inactivation of the bacterial sodium channel NaVAb

Homotetrameric bacterial voltage-gated sodium channels share major biophysical features with their more complex eukaryotic counterparts, including a slow-inactivation mechanism that reduces ion-conductance activity during prolonged depolarization through conformational changes in the pore. The bacterial sodium channel NaVAb activates at very negative membrane potentials and inactivates through a multiphase slow-inactivation mechanism. Early voltage-dependent inactivation during one depolarization is followed by late use-dependent inactivation during repetitive depolarization. Mutations that change the molecular volume of Thr206 in the pore-lining S6 segment can enhance or strongly block early voltage-dependent inactivation, suggesting that this residue serves as a molecular hub controlling the coupling of activation to inactivation. In contrast, truncation of the C-terminal tail enhances the early phase of inactivation yet completely blocks late use-dependent inactivation. Determination of the structure of a C-terminal tail truncation mutant and molecular modeling of conformational changes at Thr206 and the S6 activation gate led to a two-step model of these gating processes. First, bending of the S6 segment, local protein interactions dependent on the size of Thr206, and exchange of hydrogen-bonding partners at the level of Thr206 trigger pore opening followed by the early phase of voltage-dependent inactivation. Thereafter, conformational changes in the C-terminal tail lead to late use-dependent inactivation. These results have important implications for the sequence of conformational changes that lead to multiphase inactivation of NaVAb and other sodium channels.
Government Quality, the Adoption of IFRS and Auditor Choice: A Cross Country Analysis

We examine the association between country-level government quality and firms’ choice of external auditors. We use a firm’s choice of a Big 4 auditor as a proxy for the demand for high-quality financial reporting. Using a cross-sectional sample of 142,193 firm-year observations from 46 countries over 1998-2007, we show that government quality of a country has a significant positive effect on the likelihood of choosing Big 4 auditors by firms in that country. We also show that firms in countries with strong governments that have adopted the IFRS are more likely to choose Big 4 than non-Big 4 auditors. To our knowledge, this is the first study of its kind to provide direct evidence on the role of government quality in firms’ choice of external auditors. The results provide insights for policy makers on the importance of government quality toward improving financial reporting quality in a country.
Clinical trial design enabling E-optimal treatment rules

Medical research has evolved conventions for choosing sample size in randomized clinical trials that rest on the theory of hypothesis testing. Bayesians have argued that trials should be designed to maximize subjective expected utility in settings of clinical interest. This perspective is compelling given a credible prior distribution on treatment response, but Bayesians have struggled to provide guidance on specification of priors. We use the frequentist statistical decision theory of Wald (1950) to study design of trials under ambiguity. We show that ε-optimal rules exist when trials have large enough sample size. An ε-optimal rule has expected welfare within ε of the welfare of the best treatment in every state of nature. Equivalently, it has maximum regret no larger than ε. We consider trials that draw predetermined numbers of subjects at random within groups stratified by covariates and treatments. The principal analytical findings are simple sufficient conditions on sample sizes that ensure existence of ε-optimal treatment rules when outcomes are bounded. These conditions are obtained by application of Hoeffding (1963) large deviations inequalities to evaluate the performance of empirical success rules.
Study on Factors Affecting Separation of Xylose From Glucose By Nanofiltration Using Composite Membrane Developed From Triethanolamine (Teoa) And Trimesoyl Chloride (TMC)

Xylose is an abundant raw material coexists with other sugars that can be turned into useful products, such as ethanol, xylitol and 2, 3-butanediol by microorganism such as yeasts, bacteria, and mycelial fungi. However more than 80 % of the production cost come from production of xylose solely, where recovery of xylose relied on chromatographic separation alone. Nanofiltration offers more economical solution to currently in use chromatography method, by usage of composite membrane developed from economical active monomer, triethanolamine (TEOA). In this study, factors affecting the process, pressure, concentration of total sugars in solution, and composition of monosaccharides in total sugar, were investigated using two-level factorial analysis. The experiment was perform using Amicon Milipore stirred cell (Model 8200) with constant stirring speed at 300 rpm and temperature at ambient. Membrane was prepared by conventional interfacial polymerization of TEOA and tri-methyl chloride (TMC) on polyethersulfone (PES) porous membrane. The glucose and xylose concentration was quantified using high performance liquid chromatography (HPLC). In this study, it was found that the composition of xylose to glucose has affected the nanofiltration the most, at 63.56 %, followed by total sugar concentration at 19.52 %, pressure contributed the least at 0.033 %. An interaction between factor total sugar concentration and composition of xylose to glucose were also found to contribute 16.10 % on nanofiltration. The coefficient of determination (R2) from analysis of variance (ANOVA) study was 0.9921. In a nutshell, nanofiltration using membrane developed from TEOA and TMC as monomers on PES membrane has the ability to separate xylose from glucose. Overall in this present study it can be concluded that nanofiltration has high potential to replace currently in use chromatograhic method in xylose separation
An observational study of the outcome between early excision and resurfacing of deep thermal burns with the results of traditional dressing at a tertiary care center

Background: Patients hospitalized with burn wounds face special challenges. Host, environmental, and organism factors increase burn patient risk of developing infection and may prolong the course of infection, once acquired. Host immune, circulatory, and respiratory systems are often compromised. Most admitted burn patients have third-degree or full-thickness burns, requiring granulation and/or grafting for acceptable repair. The zone of necrosis surrounding the burned tissue may continue to expand for up to 48 hours after injury, enlarging and deepening the path for pathogen invasion. Hospital environments may contain resistant strains of pathogenic organisms. Many studies have proved early excision and grafting of burn to be the better modality of treatment when compared with other methods like conservative dressing with antibiotics etc. This study was conducted to observe that early excision is better in patients having burn surface area less than 30% when compared to conservative dressing.Methods: This is an observational study of 60 patients out of which 30 received early resection and remaining 30 were treated with conservative dressing by antibiotics and other topical ointments.Results: In this study, observation was made that early resection of burns involving less than 30% body surface area has better outcomes in various parameters than conservative dressing and this has been statistically proven.Conclusions: This study concludes that early excision and resurfacing of deep burns is beneficial than the traditional dressing of burn wounds and saves time, resources and also gives a better outcome.
The Influence of Clients' Qualities on Green Design Performance of Building Projects in Malaysia-Descriptive Study

Problem statement: In the construction industry, success of building projects greatly depends on the clients performance. The performance of clients is crucial since decisions made will influence the overall project performance. Typically, clients are represented by managerial and technical representatives during the design process. They play major roles in conveying required information to the design team regarding their future project. The quality of clients representatives has potential influence on design team performance. In designing green buildings clients attributes are critical factors to high performance of building projects. Attributes such as knowledge and experience on green buildings, commitment level to green and clients ability to participate and manage design process are the key factors to produce green design. The propose of this study to identify current performance level of clients of building projects and establish key clients attributes influencing green design performance. Approach: To achieve mentioned aim a questionnaire survey was conducted to collect dada required. A sample of 274 respondents has been covered under the study, including architects and engineers practicing design and consultancy building sectors. Prior to analysis of data WINSTEPS software were used for Rasch modeling to determine validity and reliability of date. Descriptive analysis data includes quantitative and qualitative. Results and Conclusion: Client qualities in general were low, client communication with design team; client involvement and ability to coordinate design process were moderate. However, Knowledge and experience on green design, client organization commitment to green and commitment in financing green design were low. The result indicates that most building clients have inadequate knowledge to manage design green buildings. Therefore, more education and training courses on green building are needed to cope with green design requirements. The client requires improving the coordination and involvement level to ensure all client requirements were identified. Regular meeting is the efficient method to communicate with a client.
Recycling Mixed Plastics Waste as Reductant in Ironmaking

One of the major obstacles to the implementation of an appropriate plastics recycling scheme is the inhomogeneity of many plastics waste. Accordingly, most of the existing recycling schemes require a feedstock that is reasonably pure and contains only items made from a single polymer type. However, in reality, waste plastics contain a mixture of plastic types, and are often contaminated with non-plastic items. This demands sorting out, which is expensive and highly labour intensive. In this work, the reduction of reagent grade iron oxide by mixed plastic waste (MPW) has been investigated through experiments conducted in a laboratory scale horizontal tube furnace. Composite pellets of reagent grade iron oxide (97 % Fe 2 O 3 ) with MPW [consisting of 50 wt % high density polyethylene (HDPE), 30% polypropylene (PP), 10% low density polyethylene (LDPE) and 10% polyethylene terephthalate (PET)] were rapidly heated at 1520°C under high purity argon gas and the off gas was continuously analysed for CO, CO 2 and CH 4 using an online infrared gas analyser (IR). The extent of reduction after ten minutes was determined for each carbonaceous reductant and the results were compared with the extent of reduction by conventional metallurgical coke under the same experimental conditions. The results show that iron oxide can be effectively reduced to produce metallic iron using MPW as reductant. An improvement in extent of reduction was observed over metallurgical coke and the individual polymers when MPW was used as reductant. This eliminates the need to sort out individual plastics from municipal solid waste for their effective utilisation as reductants in ironmaking. Keywords: Reduction, Metallurgical coke, Mixed plastics waste, Extent of reduction