Miracle-dz/UniFAR-FTUs huggingface dataset:
A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?

Genome sizes vary widely among species, but comprehensive explanations for the emergence of this variation have not been validated. Lynch and Conery (2003) hypothesized that genome expansion is maladaptive, and that lineages with small effective population size (Ne) evolve larger genomes than those with large Ne as a consequence of the lowered efficacy of natural selection in small populations. In addition, mating systems likely affect genome size evolution via effects on both Ne and the spread of transposable elements (TEs). We present a comparative analysis of the effects of Ne and mating system on genome size evolution in seed plants. The dataset includes 205 species with monoploid genome size estimates (corrected for recent polyploidy) ranging from 2Cx = 0.3 to 65.9 pg. The raw data exhibited a strong positive relationship between outcrossing and genome size, a negative relationship between Ne and genome size, but no detectable Ne× outcrossing interaction. In contrast, phylogenetically independent contrast analyses found only a weak relationship between outcrossing and genome size and no relationship between Ne and genome size. Thus, seed plants do not support the Lynch and Conery mechanism of genome size evolution. Further work is needed to disentangle contrasting effects of mating systems on the efficacy of selection and TE transmission.
Bundles of interest based registration of White Matter tractographies

We present an efficient and robust method for direct registration between fiber bundles of interest and the complete White Matter (WM) tractography of the same or another brain. The method does not require any previous registration between the brains, such as DTI registration, and it can be used for both intra and inter-subject registration. The algorithm is inspired by the well known iterative closest point method. Here, 3D points are replaced by feature vectors representing WM fibers, and the neighborhood is determined by the efficient approximation framework of the locality sensitive hashing. Initial results demonstrate the successful application of the proposed registration method to the automatic extraction of anatomical WM structures in un- segmented brain tractographies.
Extracting historical terms based on aligned Chinese-English parallel corpora

This paper examines the feasibility of implementing statistic-oriented term extraction and evaluation methods in extracting historical terms from aligned parallel corpora of Chinese historical classics and their translations. It proposes to take transliteration as anchor points to establish sentence-level alignment. It also investigates the approach to extract term translation pairs based on 4000 parallel sentences or segments of sentences from the corpora of the Chinese historical classic Shi Ji (Records of the Historian) and its English translations by two well-known translators. The experimental results indicate that the statistically sound algorithm can successfully extract those terms whose English translations are consistent throughout the corpus and those transliterated pairs, but fails to extract the translations of those terms that are translated differently by the two translators although the translations may be equally qualified in terms of their usage in the English language. The algorithm also fails to extract the top frequency terms which are ambiguous in meaning due to changes of its part of speech. Therefore, this paper suggests insights gained from the linguistic and translation studies perspectives can be integrated with the statistic measurements to improve the extraction and validating results.
HOTL: a higher order theory of locality

The locality metrics are many, for example, miss ratio to test performance, data footprint to manage cache sharing, and reuse distance to analyze and optimize a program. It is unclear how different metrics are related, whether one subsumes another, and what combination may represent locality completely. This paper first derives a set of formulas to convert between five locality metrics and gives the condition for correctness. The transformation is analogous to differentiation and integration used to convert between higher order polynomials. As a result, these metrics can be assigned an order and organized into a hierarchy. Using the new theory, the paper then develops two techniques: one measures the locality in real time without special hardware support, and the other predicts multicore cache interference without parallel testing. The paper evaluates them using sequential and parallel programs as well as for a parallel mix of sequential programs.
Molecular Pathways Molecular Pathways : Toll-like Receptors in the Tumor Microenvironment — Poor Prognosis or New Therapeutic Opportunity

Numerous reports have described Toll-like receptor (TLR) expression in the tumor microenvironment as it relates to cancer progression, as well as their involvement in inflammation. While TLRs mediate immune surveillance, clinical studies have associated TLR expression in the tumor with poor patient survival, indicating that TLR expression may affect cancer treatment and survival. This review will examine mechanisms in which TLR activation upregulates protumorigenic pathways, including the induction of inducible nitric oxide synthase (iNOS2) and COX2, which in turn increase TLR expression and promote a feed-forward loop leading to tumor progression and the development of more aggressive tumor phenotypes. These propagating loops involve cancer cell, stroma, and/or immune cell TLR expression. Because of abundant TLR expression in many human tumors, several TLR agonists are now in clinical and preclinical trials and some have shown enhanced efficacy when used as adjuvant with radiation, chemotherapy, or cancer vaccines. These findings suggest that TLR expression influences cancer biology and therapeutic response, which may involve specific interactions within the tumor microenvironment, including mediators of inflammation such as nitric oxide and the arachidonic acid signaling pathways. Clin Cancer Res; 19(6); 1–7. 2012 AACR.
Mechanism of the increase in cation permeability of human erythrocytes in low-chloride media. Involvement of the anion transport protein capnophorin

When human erythrocytes are suspended in low-Cl- media (with sucrose replacing Cl-), there is a large increase in both the net efflux and permeability of K+. A substantial portion (greater than 70% with Cl- less than 12.5 mM) of this K+ efflux is inhibited by the anion exchange inhibitor DIDS (4,4'-diisothiocyanostilbene-2,2'-disulfonic acid). This inhibition cannot be explained as an effect of DIDS on net Cl- permeability (Pcl) and membrane potential, but rather represents a direct effect on the K+ permeability. When cells are reacted with DIDS for different times, the inhibition of K+ efflux parallels that of Cl- exchange, which strongly indicates that the band 3 anion exchange protein (capnophorin) mediates the net K+ flux. Since a noncompetitive inhibitor of anion exchange, niflumic acid, has no effect on net K+ efflux, the net K+ flow does not seem to involve the band 3 conformational change that mediates anion exchange. The data suggest that in low-Cl- media, the anion selectivity of capnophorin decreases so that it can act as a very low-conductivity channel for cations. Na+ and Rb+, as well as K+, can utilize this pathway.
Effects of various test regimes on fatigue behaviour of PMMA bone cement: a comparative study

Numerous testing regimes have been used in vitro to assess the fatigue behaviour of acrylic bone cements. While some attempts have been made to introduce an optimal protocol that measures the fatigue life of bone cement under similar stress conditions to those exist in vivo, the effects of specific testing variables such as test specimen specification and stress parameters are still questionable. These factors can be important since inconsistency in results have been reported regarding the precise effects of other variables such as the mixing method of cement components and the resultant porosity. For a given series of testing variables; namely, specimen cross sectional shape, surface production method and stress type and level (herein collectively termed testing regime), this study investigates the effect of each variable on both the fatigue life and the fatigue crack propagation properties (fatigue behaviour) of bone cement. Testing was constantly performed in 37˚C saline under stress-controlled conditions at a frequency of 3Hz (2Hz for the CT specimens). All specimens were produced after vacuum mixing of the cement components and soaked in 37˚C saline for 1- 6 weeks. Specimens were manufactured with two cross sectional shapes: rectangular (ISO 527-2) and circular (ASTM F2118), using two production methods: direct moulding or machining. Two different bone cements were used: SmartSet GHV and CMW1. For each specimen type, at least 10 specimens were fatigued to failure at a maximum stress of 20 MPa applying either fully reversed tension-compression (R= –1) or tension-tension (R= 0.1) loading, followed by Weibull analysis. For the fully reversed loading only, at least 5 specimens were tested for each group at other three levels: ±12.5, ±15 and ±30 MPa and the four stresses were compared using S-N curves. Behaviour of fatigue cracks were assessed based on the cyclic stress-strain responses. CT specimens were used to measure the crack growth rates in the two cements. The findings of this study have emphasised the important role of the set of a testing regime variables included in testing and identified the influence of each testing variable on the fatigue behaviour of bone cement. Machining of test specimens and applying high stress levels, in particular, can lead to irrelevant findings when considering the in vivo conditions, depending also on the cement composition. While these “inappropriate” testing variables can be considered as possible reasons for the variations in fatigue results reported in previous work, it is suggested to consider the effects of these variables in future work.
Does metabolic radiolabeling stimulate the stress response? Gene expression profiling reveals differential cellular responses to internal beta vs. external gamma radiation

DNA microarray analyses were used to investigate the effect of cell‐incorporated 35S‐methionine on human colorectal carcinoma cells. This β‐radiation‐induced gene expression profile was compared with that induced by external γ‐radiation. The extent of DNA fragmentation was used as a biomarker to determine the external γ dose that was bioequivalent to that received by cells incubated in medium containing 35S‐methionine. Studies showed that 35S‐methionine at 100 µCi/mL induced a much more robust transcriptional response than γ‐radiation (2000 cGy) when evaluated 2 h after the labeling or irradiation period. The cellular response to internal β‐radiation was greater not only with respect to the number of genes induced, but also with respect to the level of gene induction. Not surprisingly, the induced genes overlapped with the set of γ‐responsive genes. However, a distinct β‐gene induction profile that included a large number of cell adhesion proteins was also observed. Taken together, these studies demonstrate that metabolic incorporation of a low energy β‐emitter, such as 35S‐methionine, can globally influence a diverse set of cellular activities that can, in turn, affect the outcome of many experiments by altering the cell cycle, metabolic, signaling, or redox status (set point) of the cell. Additional studies of the mechanism of β‐induced proliferation arrest and cell death and of the significance of its differential gene induction/repression profile in comparison to pulsed γ‐irradiation may lead to new insights into the ways in which ionizing radiation can interact with cells. —Marko, N. F. , Dieffenbach, P. B. , Yan, G. , Ceryak, S. , Howell, R. W. , McCaffrey, T. A. , Hu, V. W. Does metabolic radiolabeling stimulate the stress response? Gene expression profiling reveals differential cellular responses to internal beta vs. external gamma radiation. FASEB J. 17, 1470–1486 (2003)
Image-space Free-viewpoint Video

Image-space free-viewpoint video (FVV) is a framework for representation and coding of sparse multi-view video and subsequent re-rendering from arbitrary viewpoints. It is based on the fundamental concept of storing all information describing a scene’s visual appearance in multi-channel video images. Each pixel’s channels define different attributes of discrete point samples of observed surfaces. In this paper, we show how image-space FVV can be implemented with standard video coding tools and ready-available video coding methods can thus be reused. Besides, this representation has been adopted as extension of the MPEG-4 AFX standard. In addition to the representation, we also introduce a novel video coding technique that allows random access and progressive transmission. We evaluate this new codec in the context of FVV and compare it to state-of-the-art image and video codecs like MPEG-4 and JPEG-2000. We present results based on real-world data proving the suitability of the chosen approach.
Virtualization Usage Models Workload Isolation Once Confined to Specialized Server and Mainframe Systems, Virtualization Is Now Supported in Off-the-shelf Systems Based on Intel Architecture Hardware. Intel Virtualization Technology Provides Hardware Support for Processor Virtualization, Enabling Si

V irtualizing a computing system’s physical resources to achieve improved sharing and utilization has been well established for decades.1 Full virtualization of all system resources−including processors, memory, and I/O devices−makes it possible to run multiple operating systems on a single physical platform. In a nonvirtualized system, a single OS controls all hardware platform resources. A virtualized system includes a new layer of software, the virtual machine monitor. The VMM’s principal role is to arbitrate accesses to the underlying physical host platform’s resources so that multiple operating systems (which are guests of the VMM) can share them. The VMM presents to each guest OS a set of virtual platform interfaces that constitute a virtual machine (VM). Once confined to specialized, proprietary, highend server and mainframe systems, virtualization is now becoming more broadly available and is supported in off-the-shelf systems based on Intel architecture (IA) hardware. This development is due in part to the steady performance improvements of IA-based systems, which mitigates traditional virtualization performance overheads. Other factors include new creative software approaches that address the difficulties inherent to IA virtualization2-4 and the emergence of novel applications for virtualization in both industry and academia.
Robust Factorisation with Uncertainty Analysis

This paper proposes how the classic factorisation algorithm for affine reconstruction can be extended to be robust to outliers and proposes how the uncertainty analysis can be performed in this case. The robust estimation approach elaborated here is based on the iteratively re-weighted least-squares but the use of other robust methods is also discussed. Moreover, the uncertainty analysis presented in this paper could be similarly used in a RANSAC or LMedS extension of the factorisation algorithm. The experiments verify that the proposed approach is reliable and able to give to consistent estimates and uncertainty measure for affine structure and motion
High Fidelity Inpainting for Critical Applications Using Image Fusion

We propose a novel image restoration technique based on complementary information present in two or more images. While standalone image inpainting techniques fill the missing information artificially, use of spatiotemporal image sequence is suitable and reliable for critical applications, since it gathers the unavailable information in one image from other images in the sequence. There are two important issues to be dealt with before utilizing such sequences. Firstly, the images should be correctly registered in order to correctly access the undamaged images for in-painting the damaged one. Secondly, the illumination conditions should be taken care of, without which shadowing effects are generated since two images can differ in the illumination conditions, as well as sensor gain settings. In this work, a RANSAC based registration technique is used to perform efficient registration in presence of artefacts. Next, the dynamic range of the images are equalized to achieve illumination coherence. Further, we use fusion methods to incorporate information from all undamaged images into the damaged image. Cosmetic inpainting is used only if no other information is present. This work has uses in annotation removal from military and medical images and video, restoration of damaged video frames, etc. The results confirm the efficiency of the proposed method
Filter bank multi carrier based MIMO system for 5G wireless communication

Filter Bank Multicarrier (FBMC) transmission technique is a primary candidate for upcoming wireless communication standard 5G. It is also considered as an alternative to the famous Orthogonal Frequency Division Multiplexing (OFDM). To ensure interference free communication, OFDM utilizes Cyclic Prefix (CP) along with a rectangular pulse shaped filter. Which renders OFDM spectrally inefficient, when incorporated over large arrays of antennas. The FBMC can overcome this problem by using a different modulation scheme and a specialized prototype filter. We started this study by presenting a detailed analysis of an FBMC system. Furthermore, the FBMC system is interfaced with a Multiple Input Multiple Output (MIMO) antenna system with different antenna array sizes. We begin with a 2 X 2 antenna array and then we perform experiments with 8, 16 and 32 transmit and receive antennas. Signaling and channel specifications are different for each case. The performance of each system is measured using Zero forcing (ZF) and Minimum Mean Square Error (MMSE) equalizers. Bit Error Rate (BER) is measured against normalized Signal to Noise Ratio (SNR) or Eb/No for each system. The results of this study show that FBMC with MIMO depicts a satisfactory improvement in performance. For the 2 X 2 MIMO system MMSE outperforms the ZF equalizer. Moreover, a significant decrease in BER was observed as the array size was increased.
Electric-Field Enhancement of a Gate-All-Around Nanowire Thin-Film Transistor Memory

A high-performance gate-all-around (GAA) poly-Si nanowire (NW) SONOS-type memory thin-film transistor (TFT) is presented. The presence of the corners of the GAA structure resulted in the program speed and memory window of this device being superior to those of a planar poly-Si TFT device. When erasing, planar devices exhibit a threshold-voltage shift resulting from gate injection; the GAA device was immune to this behavior. The presence of a nonuniform electric field in the channel region during programming and erasing was confirmed through simulation. The device also exhibited superior endurance and data-retention behavior.
Fast decoding for indexation of broadcast data

Processingtime is an important factor in making a speechtran-scription systemviable for automatic indexationof radio andtele-vision broadcasts. When only concerned by the word error rate, it is common to design systems that run in 100 times real-time or more. This paper addresses issues in reducing the speech recognition time for automatic indexation of radio and TV broadcasts with the aim of obtaining reasonable performance for close to real-time operation. We investigated computational resources in the range 1 to 10xRT on commonly available platforms. Constraints on the computational resources led us to reconsider design issues, particularly those concerning the acoustic models and the decoding strategy. A new decoder was implemented which transcribes broadcast data in few times real-time with only a slight increase in word error rate when compared to our best system. Experiments with spoken document retrieval show that comparable IR results are obtained with a 10xRT automatic transcription or with manual transcription, and that reasonable per-formamce is still obtained with a 1.4xRT transcription system.
Measurements of Matrix Cracking and Delamination Caused by Impact on Composite Plates

Tests were performed measuring the locations and extents of delaminations and matrix crackings in 3 inches by 3 inches Fiberite T300/934 graphite/epoxy plates impacted by 1/2 inch diameter aluminum spheres. Plates with six ply orientations were tested ([0 16], [04/ 908/04], [03/90 10/03], [02/9012/02], [0 4/-454/454/904], and [04/45 4/604/904]). The impac tor speeds ranged from 700 to 1300 in/sec. The plates were inspected by C-scan both before and after impact. The plates were also dissected after impact and examined visually for damage In addition, the longitudinal and transverse tensile, compressive, and shear properties of the material were measured
Migration of human melanoma cells depends on extracellular pH and Na+/H+ exchange

Their glycolytic metabolism imposes an increased acid load upon tumour cells. The surplus protons are extruded by the Na+/H+ exchanger (NHE) which causes an extracellular acidification. It is not yet known by what mechanism extracellular pH (pHe) and NHE activity affect tumour cell migration and thus metastasis. We studied the impact of pHe and NHE activity on the motility of human melanoma (MV3) cells. Cells were seeded on/in collagen I matrices. Migration was monitored employing time lapse video microscopy and then quantified as the movement of the cell centre. Intracellular pH (pHi) was measured fluorometrically. Cell–matrix interactions were tested in cell adhesion assays and by the displacement of microbeads inside a collagen matrix. Migration depended on the integrin α2β1. Cells reached their maximum motility at pHe∼7.0. They hardly migrated at pHe 6.6 or 7.5, when NHE was inhibited, or when NHE activity was stimulated by loading cells with propionic acid. These procedures also caused characteristic changes in cell morphology and pHi. The changes in pHi, however, did not account for the changes in morphology and migratory behaviour. Migration and morphology more likely correlate with the strength of cell–matrix interactions. Adhesion was the strongest at pHe 6.6. It weakened at basic pHe, upon NHE inhibition, or upon blockage of the integrin α2β1. We propose that pHe and NHE activity affect migration of human melanoma cells by modulating cell–matrix interactions. Migration is hindered when the interaction is too strong (acidic pHe) or too weak (alkaline pHe or NHE inhibition).