Miracle-dz/UniFAR-FTUs huggingface dataset:
Repeats as global DNA methylation marker in bovine preimplantation embryos

DNA methylation undergoes dynamic changes and is a crucial part of the epigenetic regulation during mammalian early development. To determine the DNA methylation levels in bovine embryos, we applied a bisulfite sequencing based method aimed at repetitive sequences including three retrotransposons (L1_BT, BovB, and ERV1-1-I_BT) and Satellite I. A more accurate estimate of the global DNA methylation level compared to previous methods using only one repeat sequence, like Alu, could be made by calculation of the weighted arithmetic mean of multiple repetitive sequences, considering the copy number of each repetitive sequence. Satellite I and L1_BT showed significant methylation reduction at the blastocyst stage, while BovB and ERV1-1-I_BT showed no difference. The mean methylation level of the repetitive sequences during preimplantation development was the lowest at the blastocyst stage. No methylation difference was found between embryos cultured in 5% and 20% O-2. Because mutations of CpGs negatively influence the calculation accuracy, we checked the mutation rate of the sequenced CpG sites. Satellite I and L1_BT showed a relatively low mutation rate (1.92 and 3.72% respectively) while that of ERV1-1-I_BT and BovB was higher (11.95 and 24% respectively). Therefore we suggest using a combination of repeats with low mutation rate, taking into account the proportion of each sequence, as a relatively quick marker for the global DNA methylation status of preimplantation stages and possibly also for other cell types.
A Unified Ternary Curve Subdivision Scheme

Abstract A unified m (m > 2)-point ternary scheme with some parameter is proposed. The continuity of subdivision scheme is analyzed based on the relationship between the subdivision scheme and difference scheme. Moreover, the proposed subdivision is extended to asymmetric multi-parameter subdivision and the asymmetric schemes in four cases are presented in detail. Some examples are given to show that the presented scheme has better approximating effect.
Evaluating the Impacts of Traditional Biomass Energy Use on Agricultural Production in Sichuan, China

As crop straw and firewood are generated as by-products of food production systems, they are perceived to be sustainable energy sources that do not threaten food security by Chinese government for a long time. However, the time spent on collecting straw and firewood may create a burden on rural household, as it could reduce the available labor inputs for agricultural production, which in turn, possibly brings negative impact on food security. Building on an integrated agriculture-energy production system, a Symmetric Normalized Quadratic (SNQ) multi-output profit function (which includes labor allocations as quasi-fixed factors) is estimated to investigate the impacts of traditional biomass energy use on agricultural production in this paper. The negative signs of the calculated cross-price elasticities of supply (agricultural products and biomass energy) confirm that the relationship between biomass collection and agricultural production is competition. Moreover, the cross-price elasticities of biomass collection with respect to inputs are positive, implying that indirect link between biomass collection and agricultural production perhaps lies in household consumption decisions. The important implication of this study is that potential policy interventions for developing biomass energy in rural China could aim at enhancing food security by improving household motivation of engaging in agricultural production and slowing down the competition between biomass collection and agricultural production. It is suggested that government should attach more importance to simultaneously promote the prices of agricultural products and control the prices of intermediate inputs.
Microribbon‐Like Elastomers for Fabricating Macroporous and Highly Flexible Scaffolds that Support Cell Proliferation in 3D

Hydrogel‐based scaffolds are widely used for culturing cells in three dimensions due to their tissue‐like water content and tunable biochemical and physical properties. Most conventional hydrogels lack the macroporosity desirable for efficient cell proliferation and migration and have limited flexibility when subject to mechanical load. Here microribbon‐like elastomers that, when photocrosslinked, can form macroporous and highly flexible scaffolds that support cell proliferation in 3D are developed. These microribbons are produced by wet‐spinning gelatin solution into microfibers, followed by drying in acetone, which causes asymmetrical collapse of microfibers to form microribbon‐like structures. Gelatin microribbons are then modified using methacrylate anhydride to allow further photocrosslinking into 3D scaffolds. The macroporosity and mechanical properties of the microribbon‐based scaffold may be tuned by varying wet‐spinning rate, drying temperature, choice of drying agent, level of glutaraldehyde crosslinking, and microribbon density. When encapsulated in the microribbon‐based scaffold, human adipose‐derived stromal cells proliferated up to 30‐fold within 3 weeks. Furthermore, microribbons‐based scaffold demonstrate great flexibility and can sustain up to 90% strain and 3 MPa stress without failing. The unique mechanical properties of microribbon‐based scaffolds make them promising tools for engineering shock‐absorbing tissues such as cartilage and intervertebral discs.
Twitter Geolocation using Knowledge-Based Methods

Automatic geolocation of microblog posts from their text content is particularly difficult because many location-indicative terms are rare terms, notably entity names such as locations, people or local organisations. Their low frequency means that key terms observed in testing are often unseen in training, such that standard classifiers are unable to learn weights for them. We propose a method for reasoning over such terms using a knowledge base, through exploiting their relations with other entities. Our technique uses a graph embedding over the knowledge base, which we couple with a text representation to learn a geolocation classifier, trained end-to-end. We show that our method improves over purely text-based methods, which we ascribe to more robust treatment of low-count and out-of-vocabulary entities.
Teaching and learning page replacement algorithms using a Java-based visualization tool

This paper presents a Java-based visualization tool that uses graphical animation to convey the concepts of various page replacement algorithms. This tool is unique in a number of respects. First, it differentiates the read-access pages from the write-access ones, since the cost of replacing a page that has been modified is greater than for one that has not. Second, it allows the user to practice and test his understanding of the concepts he has learnt through a very easy-to-use graphical user interface. Third, it allows the user to compare the performance of two different algorithms or that of the same algorithm with different conditions in an easy manner. This tool can be used by teachers and students in Operating Systems courses as a teaching and learning aid or by anyone who is interested in page replacement algorithms. Key-Words: Algorithm Animation, Visualization Tool, Computer Science Education, Page Replacement Algorithms, and Operating System
Communicative Impairment After Traumatic Brain Injury: Evidence and Pathways to Recovery

Traumatic brain injury (TBI) patients show a series of communicative difficulties, loading on all the dimensions that characterize satisfying communicative interactions. This chapter has three aims: first, it reviews the current literature on this topic in order to provide a complete picture of the communicative impairment in TBI patients; second, it examines the relationship between cognitive functions i.e. executive functions and theory of mind and pragmatic deficits resulting as a consequence of traumatic brain injury; third, it reviews the current literature on treatment planning in rehabilitation therapy and provides suggestions for the clinical practice.
Study on Evaporation Characteristics of Bio-oil and its Compound Models

In this study, bio-oil was analyzed by gas chromatography mass spectrometry (GC-MS), and the evaporation characteristics of bio-oil were studied at different heating rates (10, 20, and 30 °C/min) from 35 °C to 250 °C by a thermal analyzer (TG-DSC). The TG-DSC results of bio-oil showed that the heat requirement of bio-oil during the evaporation process ranged from 2.072103 to 2.299103 J/g, and the bio-oil activation energy ranged from 1.22×104 to 3.34×104 J/mol. Moreover, four models with five compounds (methanol, water, ethanol, furfural, and phenol) were established to study the bio-oil evaporation process. By comparing the TG-DSC results of bio-oil and its models at 30 °C/min, it was shown that the optimal model was model 2, which has the following chemical composition: methanol (27.10 wt.%), water (44.96 wt.%), ethanol (16.24 wt.%), furfural (4.40 wt.%), and phenol (7.30 wt.%). Model 2 exhibited a minimal relative error in dynamic parameters and characteristic curve parameters. The errors for activation energy of the TG, activation energy of the DSC, maximum endothermic rates, and the total of the heat absorption were 3.04%, 5.88%, 2.49%, and 1.06%, respectively.
Validation of Atmospheric Infrared Sounder temperature and water vapor retrievals with matched radiosonde measurements and forecasts

[1] An evaluation of the temperature and moisture profile retrievals from the Atmospheric Infrared Sounder (AIRS) data is performed using more than 2 years of collocated data sets. The Aqua-AIRS retrievals, global radiosonde (RAOB) measurements, forecast data from the National Center for Environmental Prediction Global Forecasting System (NCEP_GFS), the European Center for Medium Range Forecast (ECMWF), and the operational retrievals from the NOAA 16 satellite Advanced TIROS Operational Vertical Sounder (ATOVS) instrument are used in this validation. Using RAOB observations as the reference, bias and RMS differences are computed for “sea,” “land,” and “all” categories for the AIRS retrievals and other collocated data sets. The results of the intercomparison reveal that temperature and water vapor retrievals from the AIRS are in very good agreement with the RAOBs. The RMS difference for clear-only cases over “sea” and “all” categories is close to the expected goal accuracies, namely, 1°K in 1 km layers for the temperature and better than 15% in 2-km layers for the water vapor in the troposphere. The overall RMS difference for the cloud-cleared cases is also close to the expected product goal accuracy except for a slight degradation at the surface. When AIRS and ATOVS retrievals are compared with the RAOBs, the AIRS temperature retrievals show an improvement over ATOVS of at least 0.5°K for all the accepted cases. Both the ECMWF and the NCEP_GFS forecasts match the RAOB temperatures within 1°K and water vapor within 14%. With respect to biases, the AIRS final retrieval shows a larger bias with the RAOBs relative to ATOVS, NCEP_GFS, and ECMWF. The bias is highly influenced by a larger bias contribution from “land” samples and shows a month-to-month and annual variation that correlates with the CO2 variations. This coupling suggests a need to include CO2 and possibly other trace gas climatologies in the AIRS initial guess to partially mitigate the effects in the final physical retrieval.
Chapter 7 NUMERICAL TRANSPORT ALGORITHMS FOR THE COMMUNITY MULTISCALE AIR QUALITY ( CMAQ ) CHEMICAL TRANSPORT MODEL IN GENERALIZED COORDINATES

The transport processes in the atmosphere primarily consist of advection and diffusion, except for the mixing of pollutants by the parameterized subgrid-scale clouds. In this chapter, numerical algorithms for advection, vertical diffusion, and horizontal diffusion implemented in the Community Multiscale Air Quality (CMAQ) chemical transport models are discussed. To provide the CMAQ system with multiscale capability, we have formulated the transport processes, both advection and diffusion, in conservation (i.e., flux) forms for the generalized coordinate system. Therefore the numerical transport algorithms implemented in CMAQ will function under a wide variety of dynamical situations and concentration distribution characteristics. Users can not only choose transport algorithms from optional modules available in CMAQ, but also are encouraged to experiment with their own algorithms to test different numerical schemes for air quality simulations. On assignment from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce. Corresponding author address: Daewon W. Byun, MD-80, Research Triangle Park, NC 27711. E-mail: bdx@hpcc.epa. gov On assignment from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce. Present Affiliation: Georgia Institute of Technology, Atlanta, GA.
Genome-wide identification and characterization of Xylanase Inhibitor Protein (XIP) genes in cereals

Xylanase inhibitor proteins (XIPs) have been reported to be involved in plant defense mechanisms, more predominantly against fungal pathogens. XIPs have mostly been well characterized in model plant species, and very little is known about their distribution, organization and evolution in cereals. In the present study, we have identified XIPs in four cereal plant species, including three major crops sorghum, maize, rice and a model species Brachypodium. The genome-wide analysis identified 10, 20, 13 and 31 XIP genes respectively for Brachypodium, sorghum, maize and rice. The number of identified genes is in well accordance with the genome size except for maize. Interestingly, most of the XIP genes were observed to be intron-less, and clustered together on the chromosomes. The XIP genes organization is much similar to the lower eukaryotes and fungi suggesting the possibility of horizontal gene transfer from the pathogen. The phylogenetic analysis of XIP revealed two major groups, and minor subgroups mostly representing gene clusters. Gene expression evaluation using publically available data suggested LOC_Os11g47500 and LOC_Os11g47510are candidate genes for resistance against Magnaporthe grisea pathogen in rice. The information provided here would be helpful for the identification of candidate resistance genes in other cereals.
Correlation of light and electron microscopy for immunogold staining . GFP immunogold , tool in biological research

Due to its stable expression, GFP is widely used as a cell marker in stem cell transplantation experiments. Localizing transplanted cells, distinguishing them from endogenous cells, and following their fate in vivo is crucial for these studies. GFP transgenics are also widely applied in stem cell research to mark specific cell types or to analyze gene expression patterns. Several techniques are available that allow the detection of GFP cells, but frequently, a fine ultrastructural analysis is needed. Unfortunately, electron microscopy processing prevents GFP post-embedding immunodetection, thus pre-embedding techniques are unavoidable. However, quality pre-embedding immunogold staining results in minimal tissue penetration, making labeled cell identification difficult. In order to solve this problem, serial semithin sections can be re-embedded for electron microscopy analysis. Independently of pre-embedding immunostaining, semithin section reembedding can be a useful tool for a fine ultrastructural analysis of specific cells studied under the light microscope. Here we describe the methods for quality pre-embedding immunogold staining and for semithin section re-embedding necessary for electron microscope observation.
Running the Gauntlet: Inhibitory Effects of Algal Turfs on the Processes of Coral Recruitment

Mortality of corals is increasing due to bleaching, disease and algal overgrowth. In the Caribbean, low rates of coral recruitment contribute to the slow or undetectable rates of recovery in reef ecosystems. Although algae have long been suspected to interfere with coral recruitment, the mechanisms of that interaction remain unclear. We experimentally tested the effects of turf algal abundance on 3 sequential factors important to recruitment of corals: the biophysical delivery of planktonic coral larvae, their propensity to settle, and the availability of microhabitats where they survive. We deployed coral settlement plates inside and outside damselfish Stegastes spp. gardens and cages. Damselfish aggression reduced herbivory from fishes, and cages became fouled with turf algae, both locally increasing algal biomass surrounding the plates. This reduced flushing rates in nursery microhabitats on the plate underside, limiting larvae available for settlement. Coral spat settled preferentially on an early successional crustose coralline alga Titanoderma prototypum but also on or near other coralline algae, biofilms, and calcareous polychaete worm tubes. Post-settlement survival was highest in the fully grazed, lowest algal biomass treatment, and after 27 mo ‘spat’ densities were 73% higher in this treatment. The ‘gauntlet’ refers to the sequence of ecological processes through which corals must survive to recruit. The highest proportion of coral spat successfully running the gauntlet did so under conditions of low algal biomass resulting from increased herbivory. If coral recruitment is heavily controlled at very local scales by this gauntlet, then coral reef managers could improve a reef’s recruitment potential by managing for reduced algal biomass.
Measuring Decreasing and Increasing Impatience

Many studies show that time preference data from experiments and surveys are related to field behavior. Time preference measures in these studies typically depend simultaneously on utility curvature, the level of impatience, and the change in the level of impatience. Thus, these studies do not allow one to establish which of these three components drive(s) the field behavior of interest. Of these components, the change in the level of impatience is theoretically thought to be the main driver of time inconsistencies and self-control problems. To test this theoretical presumption, one has to measure the change in the level of impatience independently from utilities and levels of impatience. This paper introduces a measure of the degree of decreasing impatience, the DI-index. It measures the change of impatience independently from the level of impatience and independently from utility. It can also be used to test various discounting models. An experiment finds no correlation between the degree of decreasing impatience and self-reported self-control problems in daily life, suggesting that changing impatience is not the sole driver of self-control problems.
Simplified converters models for the analysis and simulation of large transmission systems Using 100% power electronics

In this paper, a model order reduction method is proposed, to simplify power electronics converters and allow simulating large transmission systems using 100% power electronics. Unlike existing methods it keeps the system's physical structure, thus making the simulation and the analysis more flexible. This method is validated on a two-converter system and proves to be both conservative and accurate.
Assessing Systemic Fragility - A Probabilistic Perspective

We outline a procedure for consistent estimation of marginal and joint default risk in the euro area financial system. We interpret the latter risk as the intrinsic financial system fragility and derive several systemic fragility indicators for euro area banks and sovereigns, based on CDS prices. Our analysis documents that although the fragility of the euro area banking system had started to deteriorate before Lehman Brothers' file for bankruptcy, investors did not expect the crisis to affect euro area sovereigns' solvency until September 2008. Since then, and especially after November 2009, joint sovereign default risk has outpaced the rise of systemic risk within the banking system.
Compresso: Pragmatic Main Memory Compression

Today, larger memory capacity and higher memory bandwidth are required for better performance and energy efficiency for many important client and datacenter applications. Hardware memory compression provides a promising direction to achieve this without increasing system cost. Unfortunately, current memory compression solutions face two significant challenges. First, keeping memory compressed requires additional memory accesses, sometimes on the critical path, which can cause performance overheads. Second, they require changing the operating system to take advantage of the increased capacity, and to handle incompressible data, which delays deployment. We propose Compresso, a hardware memory compression architecture that minimizes memory overheads due to compression, with no changes to the OS. We identify new data-movement trade-offs and propose optimizations that reduce additional memory movement to improve system efficiency. We propose a holistic evaluation for compressed systems. Our results show that Compresso achieves a 1.85x compression for main memory on average, with a 24% speedup over a competitive hardware compressed system for single-core systems and 27% for multi-core systems. As compared to competitive compressed systems, Compresso not only reduces performance overhead of compression, but also increases performance gain from higher memory capacity.
Ascorbic Acid and/or 24-Epibrassinolide Trigger Physiological and Biochemical Responses for the Salt Stress Mitigation in Potato (Solanum tuberosum L.)

In the present study, we examined the role of ascorbic acid (AsA, vitamin C) and/or 24-epibrassinolide (EBL, an active BR) in mitigation of salt-induced stress in potato ( Solanum tuberousum L). The 10-d-old plants were exposed to 150 mM NaCl and they were subsequently treated by ASA and/or EBL. The salt stress reduced significantly the plant growth, tuber yield, total chlorophyll and increased proline content and electrolyte leakage in the leaves. Toxic effects induced by salt stress were completely overcome by the combined exogenous application of AsA and EBL. The AsA and/or EBL treatments improved the growth parameters of the salt treated plants, such as shoot length, tuber number and size, fresh and dry mass and other physiological parameters. Our data also indicated that applications of AsA and EBL up-regulated the stress regulating plant hormone such as IAA, IBA and activities of the antioxidant enzymes, such as catalase (CAT), peroxidase (POX), superoxide dismutase (SOD), ascorbate peroxidase (APX) and under salt stress. Int J Appl Sci Biotechnol, Vol 3(4): 655-667
Superconducting MoSi nanowires

We have fabricated disordered superconducting nanowires of molybdenium silicide. A molybdenium nanowire is first deposited on top of silicon, and the alloy is formed by rapid thermal annealing. The method allows tuning of the crystal growth to optimize e.g. the resistivity of the alloy for potential applications in quantum phase slip (QPS) devices and superconducting nanowire single-photon detectors. The wires have effective diameters from 42 to 79 nm, enabling the observation of crossover from conventional superconductivity to regimes affected by thermal and quantum fluctuations. In the smallest diameter wire and at temperatures well below the superconducting critical temperature, we observe residual resistance and negative magnetoresistance, which can be considered as fingerprints of QPSs.