Miracle-dz/UniFAR-FTUs huggingface dataset:
Grafting Triggers Differential Responses between Scion and Rootstock

Grafting is a well-established practice to facilitate asexual propagation in horticultural and agricultural crops. It has become a method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. The objective of this study was to investigate differences in gene expression between the organs of the scion and rootstock of a homograft (Arabidopsis thaliana). MapMan and Gene Ontology enrichment analysis revealed differentially expressed genes from numerous functional categories related to stress responses in the developing flower buds and leaves of scion and rootstock. Meta-analysis suggested induction of drought-type responses in flower buds and leaves of the scion. The flower buds of scion showed over-representation of the transcription factor genes, such as Homeobox, NAC, MYB, bHLH, B3, C3HC4, PLATZ etc. The scion leaves exhibited higher accumulation of the regulatory genes for flower development, such as SEPALLATA 1–4, Jumonji C and AHL16. Differential transcription of genes related to ethylene, gibberellic acid and other stimuli was observed between scion and rootstock. The study is useful in understanding the molecular basis of grafting and acclimation of scion on rootstock.
Gradient field distributions for the registration of images

This paper introduces a new method to register images that are rotated and translated with respect to each other. The method works by transforming each image to a gradient distribution space. This space represents the likelihood of finding a particular gradient in the image and is invariant to translation. Once transformed the rotation between the images is efficiently found using correlation. Unlike Fourier based methods, phase information is retained in the gradient distribution space, thus a larger class of images can be accurately registered. The method is computationally efficient and does not require nonlinear optimization or iterative methods. Furthermore, large rotations and translations can easily be handled.
Intermediate-velocity gas observed towards the Shajn 147 SNR

We present high-resolution spectra (R ∼ 3k m s −1 ) of the interstellar Na  and Ca  interstellar absorption lines observed towards 3 early-type stars with distances of 360 to 1380 pc along the line-of-sight towards the 800 pc distant Shajn 147 (S147) Supernova Remnant (SNR). These data are supplemented with far-UV (912-1180 A) aborption spectra of HD 36665 and HD 37318 recorded with the NASA Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. The observations reveal intermediate-velocity (IV) absorption features at Vhelio =+ 92 km s −1 towards HD 37318 and at Vhelio = −65 and −52 km s −1 towards HD 36665, in addition to several other gas cloud components with lower velocity. These IV components can be associated with the expansion of the SNR that has disrupted the surrounding interstellar gas. The IV component at V =+ 92 km s −1 seen towards HD 37318 was detected only in the far-UV lines of Fe  and N , suggesting that it is composed mainly of warm and ionized gas. The two IV components observed towards HD 36665 were detected in Na  ,C a ,N  ,N  ,O  and Fe , indicating that it is composed of both neutral and ionized gas shells. Highly ionized gas was detected in the O λ 1032 A absorption line at V ∼ +40 km s −1 towards both stars. This hot and highly ionized gas component is characterized by a columnn density ratio of N(C )/N(O ) < 0.27, which is consistent with that predicted by current models of evolved SNRs. However, we cannot preclude its origin in the interstellar medium in line-of-sight to S147. Column-density ratios of (Mg/Fe), (Al/Si),(Si/Fe), (N/Fe), (O/Fe) and (Na/Ca) have been derived for the IV gas components detected towards S147. Similar ratios have also been derived for fast-moving gas observed towards two other SNRs in order to gain some insight into the behavior of element abundances in the disturbed interstellar gas associated with these regions. In all cases except for Na and Ca, these elements appear to be present with near-solar abundance ratios.
Reducing power consumption in graphic intensive Android applications

With the ubiquity and increased usage of mobile devices with higher processing capability, power consumption in such devices is an important issue. In this paper we propose a software based approach to reduce the power consumption of an Android application which is having higher graphics or rendering requirements. Graphics intensive applications such as games, internet browser and video player contribute most in draining the battery. Therefore, we concentrate most on such applications for reducing the power consumption. Our approach involves removing the surface view and directly utilizing the application's main window surface. We conduct an experiment to measure the power consumption when running an application with and without using surface view, and show that we get an improvement in the consumption. We also discuss about advantages and problems of the proposed method along with some possible solutions.
Accurate formula for P-values of gapped local sequence and profile alignments.

A simple general approximation for the distribution of gapped local alignment scores is presented, suitable for assessing significance of comparisons between two protein sequences or a sequence and a profile. The approximation takes account of the scoring scheme (i.e. gap penalty and substitution matrix or profile), sequence composition and length. Use of this formula means it is unnecessary to fit an extreme-value distribution to simulations or to the results of databank searches. The method is based on the theoretical ideas introduced by R. Mott and R. Tribe in 1999. Extensive simulation studies show that score-thresholds produced by the method are accurate to within +/-5 % 95 % of the time. We also investigate factors which effect the accuracy of alignment statistics, and show that any method based on asymptotic theory is limited because asymptotic behaviour is not strictly achieved for many real protein sequences, due to extreme composition effects. Consequently, it may not be practicable to find a general formula that is significantly more accurate until the sub-asymptotic behaviour of alignments is better understood.
The U.S. Current Account: The Other Deficit

Considerable attention has been focused recently on the size and persistence of the U.S. budget deficit. Somewhat lost in the headlines is growing concern among many economists and policymakers over "the other deficit"--the U.S. current account deficit. Before 1982, U.S. current account deficits were small and temporary, as imports of goods and services rarely exceeded exports for an extended period. Since 1982, however, this deficit has increased significantly and many analysts expect the deficit to remain high well into the next century. > Large current account deficits pose both a short-term risk and a long-term problem for the United States. At present, the United States depends on a commensurately large flow of foreign capital into U.S. markets to finance the current account deficit. If market sentiment were to shift against the United States, higher interest rates and a lower exchange value of the dollar might be necessary to continue to attract foreign capital. In the long term, because financing a chronic deficit requires the United States to borrow from abroad, future interest payments on this debt could lower the standard of living in the United States. > Hakkio examines the current account deficit and its implications. First, he discusses why the current account deficit became large and persistent in the early 1980s. Second, he analyzes the short-term risk that current account deficits pose for the U.S. economy. Finally, he analyzes the long-term problem associated with a chronic current account deficit.
Sex‐specific correlation between heterozygosity and clone size in the trematode Schistosma mansoni

The mode of reproduction (sexual and/or asexual) and the mating system determine the patterns of gene transmission and genotype formation across generations. Schistosoma mansoni is a dioecious trematode that necessarily alternates sexual and asexual reproduction during its life cycle. In a previous study of the distribution of S. mansoni genetic variability within and between definitive host individuals, we noticed that deleting multilocus genotypes from each infrapopulation so as to keep only one copy of each multilocus genotype, seemed to have a substantial effect on FIS values. More precisely, female FIS increased when repeated genotypes were removed whereas no effect was observed on male FIS. This suggested that multilocus genotypes at high frequency tended to be more heterozygous. The aim of the present study is specifically to test and analyse this phenomenon. We demonstrate that the number of repetitions per clone correlates with individual heterozygosity. This effect is however, sex‐specific: only female clone size correlates with heterozygosity. We discuss this phenomenon in relation to the heterozygosity–fitness relationship and the sex‐specific response to inbreeding depression.
Running head: Title:

Running head: 1 Transcriptome coverage and microarray sensitivity 2 3 4 Title: 5 A rapid method for computationally inferring 6 transcriptome coverage and microarray sensitivity 7 8 9 Authors: 10 A. Reverter, S. M. McWilliam, W. Barris and B. P. Dalrymple 11 12 Bioinformatics Group, CSIRO Livestock Industries, 13 Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, QLD 4067, Australia 14 15 16
A Comprehensive Review on Blog Mining under a Cross-Disciplinary Framework

Nowadays, blog has been playing a more and more important role in human life as the internet evolves dramatically. Academia has seen an research burst on blog since 2002, not only in the area of computer science like IR and web mining, but also in the area of social sciences. We present a blog-centered framework here to abstract and generalize current researches on blog mining, with the intention of providing a clear image on blog-focused research area.
Calculating Total System Availability

In a mission critical application, “Availability” is the very first requirement to consider. Thus understanding what it is, what would affect it, and how to calculate it is vital. Although many methods have been proposed to calculate the availability of a device and/or a simple system, calculating the availability of a Business Application within a very complex organization is not still easily achievable. In this project, we would be proposing a method to enable the IT management team of KLM, to predict their Business Application availability based on the configuration and the components used in their infrastructure. System Availability, Reliability Engineering, MTBF, MTTR, Failure, Network, Application
Developing an efficient digital image watermarking for smartphones

In recent years, Smartphone usage has been increasing rapidly to the point where it surpassed all other electronic devices. Multimedia sharing and Image/Video capturing are amongst the most utilized functionalities of smartphones. Smartphones and Internet availability made the capture, transmission and storage of digital data very easy and convenient. The simplicity, connectivity, and strong capabilities of such devices make it very hard to protect the privacy and Intellectual Property (IP) of digital multimedia. While all types of digital multimedia are at risk, digital images are severely affected. Editing and converting digital images can be done quite easily, and hence protecting them becomes even harder. Digital image watermarking is a technique used to authenticate and protect the IP of digital images. In this paper we propose an efficient and flexible digital watermarking system that runs on Android devices. The system uses RAW images (a feature of the most recent Android software, called Lollipop) to embed a watermark at an early stage before any modification and conversion of the image. The system incorporates public-key cryptography for increased protection. A simple and robust watermarking technique is utilized for efficiency. Other watermarking techniques are offered for flexibility. Finally, the system uses the inherent features of the Android operating system to run in parallel and be available to other applications.
Morphometric analysis of trabecular bone thickness using different algorithms

Investigations have been carried out with the goal of assessing the trabecular bone thickness of biological samples using images obtained by micro-computed tomography and magnetic resonance imaging. There is no conventional definition of trabecular bone thickness, and many methods may be involved in determining it. However, the results of the available algorithms or software packages differ considerably from each other. This paper determines trabecular bone thickness on the basis of several algorithms. A deep understanding of the performance of different methods is achieved by studying pseudo-three-dimensional images of both geometrical models of well-defined thickness and real bone samples with different bone densities. The models facilitate comparisons between the algorithms or software packages. Comparison of the results obtained from these commercial software packages and other state-of-the-art algorithms shows that the thickness, spatial distribution, and shape of an object affect each result differently, but in a significant manner. This is primarily due to variations in the thresholding algorithms used to distinguish object area elements (pixels/voxels) from the background, or non-object, region. Additionally, the results show that the average difference in thickness measurements can vary by up to 102.34% for models and 46.49% for real bone samples. This data shows that the differences in measurements of the trabecular bone thickness due simply to the algorithm involved are remarkable. Therefore, biomedical engineers and scientists should be careful to select the algorithm that is most compatible with their specific application.
Efficient multistage implementation of rational sampling rate converter

In Digital audio processing, there are multiple standard sampling rates, for example, 48kHz for studio work, 44.1kHz for compact disk(CD) mastering. Therefore, sampling rate conversion is needed to interchange signals from one field to another. A rational sampling rate conversion by L/M can be done cascading an L-fold up-sampler and an M-fold down-sampler with a linear phase FIR lowpass filter in the middle. When both L and M have large values, the lowpass filters are required to have an extremely narrow normalized bandwidth and a sharp transition characteristic, causing difficulty in design and implementation. This paper describes a technique to overcome this difficulty for the case both L and M are composite numbers, giving an multistage converter structure where each stage is consisting of an up-sampler and a down-sampler, both of a small conversion ratios, with a filter having not so sharp normalized transition characteristic in the middle, remarkably reduced total computation complexity.
Quantum-Bayesian Coherence

In a quantum-Bayesian take on quantum mechanics, the Born Rule cannot be interpreted as a rule for setting measurement-outcome probabilities from an objective quantum state. But if not, what is the role of the rule? In this paper, we argue that it should be seen as an empirical addition to Bayesian reasoning itself. Particularly, we show how to view the Born Rule as a normative rule in addition to usual Dutch-book coherence. It is a rule that takes into account how one should assign probabilities to the consequences of various intended measurements on a physical system, but explicitly in terms of prior probabilities for and conditional probabilities consequent upon the imagined outcomes of a special counterfactual reference measurement. This interpretation is seen particularly clearly by representing quantum states in terms of probabilities for the outcomes of a fixed, fiducial symmetric informationally complete (SIC) measurement. We further explore the extent to which the general form of the new normative rule implies the full state-space structure of quantum mechanics. It seems to get quite far.
Impact of ISO 9000 on organizational climate: Strategic change management experience of an Indian organization

Purpose - ISO 9000 yields visible and concrete benefits to organizations in the form of sustained product quality, enhanced market image, increased customer satisfaction, and long-term profitability. However, the derivative impact of ISO 9000 on the human side of the organization, especially its impact on the internal human environment, has been only scantily researched. The purpose of this study is to explore how the process of ISO 9000 implementation transforms the components of organizational climate, particularly the climate motives existing in an organization. Design/methodology/approach - ISO 9000 system was deemed as the independent variable that could induce changes in organizational climate, the dependent variable. Climate was measured both before and after the implementation of ISO 9000, using Pareek's MAO-C instrument. Based on the scores obtained for the constituent climate motives, the patterns of organizational climate that prevailed in an organization both before and after ISO implementation were deciphered. Findings - Results reveal that as a result of ISO 9000 implementation the dysfunctional organizational climate motives such as control, dependency, and affiliation undergo a u-turn transformation giving way to the functional and conducive climate motives such as achievement, expert influence, and extension. Originality/value - The study endeavors to throw light on the favorable impact that ISO 9000 may have on organizational climate of organizations. The findings tend to prognosticate that when implemented well the ISO 9000 system could function not just as a quality enhancement instrument but in addition as a useful tool for strategic change management that could truly hold the potential for transforming both the character and performance of organizations.
Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence

For decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic mis-folding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field.
Ultraviolet B but not Ultraviolet A Radiation Initiates Melanoma

Cutaneous malignant melanoma is one of the fastest increasing cancers with an incidence that has more than doubled in the last 25 years. Sunlight exposure is strongly implicated in the etiology of cutaneous malignant melanoma and the UV portion of the sunlight spectrum is considered responsible. Data are, however, conflicting on the roles of ultraviolet B [UVB; 280–320 nanometers (nm)] and ultraviolet A (UVA; 320–400 nm), which differ in their ability to initiate DNA damage, cell signaling pathways and immune alterations. To address this issue, we have used specialized optical sources, emitting isolated or combined UVB or UVA wavebands or solar simulating radiation, together with our hepatocyte growth factor/scatter factor-transgenic mouse model of UV-induced melanoma that uniquely recapitulates human disease. Only UVB-containing sources initiated melanoma. These were the isolated UVB waveband (>96% 280–320 nm), the unfiltered F40 sunlamp (250–800 nm) and the solar simulator (290–800 nm). Kaplan-Meier survival analysis indicated that the isolated UVB waveband was more effective in initiating melanoma than either the F40 sunlamp or the solar simulator (modified log rank P < 0.02). The latter two sources showed similar melanoma effectiveness (P = 0.38). In contrast, transgenic mice irradiated with either the isolated UVA waveband (>99.9% 320–400 nm, 150 kJ/m2), or an F40 sunlamp filtered to remove > 96% of the UVB, responded like unirradiated control animals. We conclude that, within the constraints of this animal model, UVB is responsible for the induction of mammalian cutaneous malignant melanoma whereas UVA is ineffective even at doses considered physiologically relevant. This finding may have major implications with respect both to risk assessment from exposure to solar and artificial UVB, and to development of effective protection strategies against melanoma induction by UVB. Moreover, these differences in wavelength effectiveness can now be exploited to identify UV pathways relevant to melanomagenesis.
Homocysteine and the Risk of Ischemic Stroke in a Triethnic Cohort: The Northern Manhattan Study

Background and Purpose— The level of total homocysteine (tHcy) that confers a risk of ischemic stroke is unsettled, and no prospective cohort studies have included sufficient elderly minority subjects. We investigated the association between mild to moderate fasting tHcy level and the incidence of ischemic stroke, myocardial infarction, and vascular death in a multiethnic prospective study. Methods— A population-based cohort was followed for vascular events (stroke, myocardial infarction, and vascular death). Baseline values of tHcy and methylmalonic acid were measured among 2939 subjects (mean age, 69±10; 61% women, 53% Hispanics, 24% blacks, and 20% whites). Cox proportional models were used to calculate hazard ratios (HRs) and 95% CIs in tHcy categories after adjusting for age, race, education, renal insufficiency, B12 deficiency, and other risk factors. Results— The adjusted HR for a tHcy level ≥15 μmol/L compared with <10 μmol/L was greatest for vascular death (HR=6.04; 95% CI, 3.44 to 10.60), followed by combined vascular events (HR=2.27; 95% CI, 1.51 to 3.43), ischemic stroke (HR=2.01; 95% CI, 1.00 to 4.05), and nonvascular death (HR=2.02; 95% CI, 1.31 to 3.14). Mild to moderate elevations of tHcy of 10 to 15 μmol/L were not significantly predictive of ischemic stroke, but increased the risk of vascular death (2.27; 95% CI, 1.44 to 3.60) and combined vascular events (1.42; 95% CI, 1.06 to 1.88). The effect of tHcy was stronger among whites and Hispanics, but not a significant risk factor for blacks. Conclusions— Total Hcy elevations above 15 μmol/L are an independent risk factor for ischemic stroke, whereas mild elevations of tHcy of 10 to 15 μmol/L are less predictive. The vascular effects of tHcy are greatest among whites and Hispanics, and less among blacks.