Miracle-dz/UniFAR-FTUs huggingface dataset:
A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines

LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the transformed state in tumor cells.
Evaluation of Memoryless Simplification

We investigate the effectiveness of the memoryless simplification approach described by Lindstrom and Turk (1998). Like many polygon simplification methods, this approach reduces the number of triangles in a model by performing a sequence of edge collapses. It differs from most recent methods, however, in that it does not retain a history of the geometry of the original model during simplification. We present numerical comparisons showing that the memoryless method results in smaller mean distance measures than many published techniques that retain geometric history. We compare a number of different vertex placement schemes for an edge collapse in order to identify the aspects of the memoryless simplification that are responsible for its high level of fidelity. We also evaluate simplification of models with boundaries, and we show how the memoryless method may be tuned to trade between manifold and boundary fidelity. We found that the memoryless approach yields consistently low mean errors when measured by the Metro mesh comparison tool. In addition to using complex models for the evaluations, we also perform comparisons using a sphere and portions of a sphere. These simple surfaces turn out to match the simplification behaviors for the more complex models that we used.
Transport and retention of silver nanoparticles in granular media filtration

For engineered nanoparticles that are being introduced into the environment, a considerable amount of research has been conducted on the transport of nanoparticles in natural and engineered systems, especially in granular media filtration. Most studies on the transport model of nanoparticles in granular media filtration have focused on numerical simulation of particle behavior; this research was designed to test the model expectations with experimental evidence. The aim of study was to evaluate the widely used colloidal filtration model using experimental results from the transport and capture of nanoparticles in granular media filtration. A series of filtration tests was conducted under varying physical parameters such as particle size, filter media size, filter depth, and filtration velocity. To scrutinize the effect of physical parameters, the chemical effect was minimized by selecting the spherical branched polyethylenimine (BPEI) capped silver nanoparticles (AgNPs) as a positively charged nanoparticle to avoid electrostatic repulsion with the negatively charged filter media. The ionic strength and pH of the test solution were controlled to prevent the aggregation of AgNPs during the filtration test period. Overall, the experimental results fit the model quite well, but some deviation from the model became apparent as the particle size decreased. This result demonstrates that the behavior of nanoparticles could be generally similar to the particles greater than nano range; however, a distinctive nature of nanoparticle transport could appear in smaller size ranges.
A Simple and Powerful Method for the Estimation of Intervention Effects on Serological Endpoints Using Paired Interval-Censored Data

Clinical trials often use a binary “fold increase” endpoint defined according to the ratio of interval-censored measurement at end-of-study to that at baseline. We propose a simple yet principled analytic approach based on the linear mixed-effects model for interval-censored data for the analysis of such paired measurements. Having estimated the model parameters, the risk ratio can be estimated by explicit composite estimand and the variance is estimated using the delta method. The estimation can be implemented using the existing procedures in popular statistical software. We use antibody data from the Chloroquine for Influenza Prevention Trial for illustration.
A New Approach for Clustered MCs Classification with Sparse Features Learning and TWSVM

In digital mammograms, an early sign of breast cancer is the existence of microcalcification clusters (MCs), which is very important to the early breast cancer detection. In this paper, a new approach is proposed to classify and detect MCs. We formulate this classification problem as sparse feature learning based classification on behalf of the test samples with a set of training samples, which are also known as a “vocabulary” of visual parts. A visual information-rich vocabulary of training samples is manually built up from a set of samples, which include MCs parts and no-MCs parts. With the prior ground truth of MCs in mammograms, the sparse feature learning is acquired by the l P-regularized least square approach with the interior-point method. Then we designed the sparse feature learning based MCs classification algorithm using twin support vector machines (TWSVMs). To investigate its performance, the proposed method is applied to DDSM datasets and compared with support vector machines (SVMs) with the same dataset. Experiments have shown that performance of the proposed method is more efficient or better than the state-of-art methods.
Flexibility of Various Nickel-Titanium Rotary Endodontic Files

Introduction: Nickel-titanium rotary files were originally developed to allow for greater flexibility when instrumenting root canals. The increased flexibility of nickel-titanium instruments allowed operators to negotiate canal curvatures with greater ease. File design is continually changing. Manufacturers are trying to produce files that will work more efficiently and safely. Knowing the properties of files marketed is especially important in helping to choose an appropriate file system. Current ISO standards require force measurements at a static point along the file. The purpose of this study was to evaluate the flexibility of four different nickel-titanium files at three different points along the file. Materials and Methods: Flexibility of four different nickel-titanium rotary files (EndoSequence, ProFile, Vortex, and Vortex Blue) was measured. Each file was clamped at 3mm, 5mm, or 7mm (n = 10/length/file) and a universal testing machine was used to bend the files to a maximum deflection of 4.5mm. All data were statistically analyzed by two-way analysis of variance and post-hoc Tukey test (P = 0.05) to determine any significant differences. Results: Statistically significant (P < 0.05) differences were present. In general, ProFile was the stiffest, displaying the greatest force and bending moment values. Vortex Blue was significantly more flexible, with lower force needed for deflection and bending moments. Conclusion: Vortex Blue files showed greater flexibility compared with the other nickel-titanium rotary files studied.
Mining the Web for Relations between Digital Devices using a Probabilistic Maximum Margin Model

Searching and reading the Web is one of the principal methods used to seek out information to resolve problems about technology in general and digital devices in particular. This paper addresses the problem of text mining in the digital devices domain. In particular, we address the task of detecting semantic relations between digital devices in the text of Web pages. We use a Na¨ıve Bayes model trained to maximize the margin and compare its performance with several other comparable methods. We construct a novel dataset which consists of segments of text extracted from the Web, where each segment contains pairs of devices. We also propose a novel, inexpensive and very effective way of getting people to label text data using a Web service, the Mechanical Turk. Our re-sults show that the maximum margin model consistently outperforms the other methods.
Agonist-induced phosphorylation of the angiotensin AT1a receptor is localized to a serine/threonine-rich region of its cytoplasmic tail.

The agonist-induced phosphorylation sites of the rat AT1a angiotensin receptor were analyzed using epitope-tagged mutant receptors expressed in Cos-7 cells. Angiotensin II-stimulated receptor phosphorylation was unaffected by truncation of the cytoplasmic tail of the receptor at Ser342 (Delta342) but was abolished by truncation at Ser325 (Delta325). Truncation at Ser335 (Delta335), or double-point mutations of Ser335 and Thr336 to alanine (ST-AA), reduced receptor phosphorylation by approximately 50%, indicating that in addition to Ser335 and/or Thr336, amino acids within the Ser326-Thr332 segment are also phosphorylated. Agonist-induced phosphorylation of the ST-AA and Delta335 receptors was partially inhibited by staurosporine, suggesting that the single protein kinase C consensus site in the Ser326-Thr332 segment (Ser331) is phosphorylated. The impairment of receptor phosphorylation was broadly correlated with the attenuation of agonist-induced internalization rates (Delta325 < Delta335 < ST-AA < Delta342 < wild-type) and with the increasing rank order of magnitude of inositol phosphate production normalized to an equal number of receptors (Delta325 > Delta335 > ST-AA = Delta342 > wild-type). These results demonstrate that agonist-induced phosphorylation of the AT1a receptor is confined to an 11-amino-acid serine/threonine-rich segment of its carboxyl-terminal cytoplasmic tail and implicate this region in the mechanisms of receptor internalization and desensitization.
Seismic Anisotropy in Salt Structures Due to Preferred Crystal Orientation

Texture analysis of natural rock salt and experimentally deformed halite have shown that lattice preferred orientation of halite crystals does occur. The elastic parameters for a range of halite polycrystalline aggregates are calculated using orientation distribution functions. These are used to construct seismic models which are ray-traced through to investigate the potential effects of seismic anisotropy in salt structures. Anisotropic salt models show significant variation in travel time from the isotropic salt model and large shear-wave splitting is predicted.
Microtubule-Mediated Inositol Lipid Signaling Plays Critical Roles in Regulation of Blebbing

Cells migrate by extending pseudopods such as lamellipodia and blebs. Although the signals leading to lamellipodia extension have been extensively investigated, those for bleb extension remain unclear. Here, we investigated signals for blebbing in Dictyostelium cells using a newly developed assay to induce blebbing. When cells were cut into two pieces with a microneedle, the anucleate fragments vigorously extended blebs. This assay enabled us to induce blebbing reproducibly, and analyses of knockout mutants and specific inhibitors identified candidate molecules that regulate blebbing. Blebs were also induced in anucleate fragments of leukocytes, indicating that this assay is generally applicable to animal cells. After cutting, microtubules in the anucleate fragments promptly depolymerized, followed by the extension of blebs. Furthermore, when intact cells were treated with a microtubule inhibitor, they frequently extended blebs. The depolymerization of microtubules induced the delocalization of inositol lipid phosphatidylinositol 3,4,5-trisphosphate from the cell membrane. PI3 kinase-null cells frequently extended blebs, whereas PTEN-null cells extended fewer blebs. From these observations, we propose a model in which microtubules play a critical role in bleb regulation via inositol lipid metabolism.
A macrotask-level unlimited speculative execution on multiprocessors

The purpose of this paper is to propose a new fast execution scheme of FORTRAN programs. The proposed scheme enables the fast initiation of macrotask when ita data dependence are satisfied even if the control flow has not been reached. The previous schemes to parallelize a program including conditional branches have a number of problems 1) Though the theoretical speedup ratio is up to N when N conditional branches are jumped on either a VLIW or a superscalstr machine, the number of N is restricted up to the number of ALUs on a chip, 2) Since conventional control schemes use a few processors to control macrotasks, the overhead to control them is large. The proposed scheme solves these problems 1) The proposed scheme enables speculative execution between coarse grain tasks, i.e., macro tasks, on multiprocessors by jumping many conditional branches, 2) A distributed control scheme is proposed and implemented on the EM-4 multiprocessor to decrease the control overhead of macrotasks. Preliminary evaluations show that the control overhead of the proposed scheme is smaller than that of the other control schemes. Moreover, it is confirmed that the distributed control can be implemented by using software when the average macrotssk execution time is larger than 14.4ps on the EM-4 multiprocessor.
Dandruff Is Associated with Disequilibrium in the Proportion of the Major Bacterial and Fungal Populations Colonizing the Scalp

The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject’s were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal) and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p<0.05). These results suggested for the first time using molecular methods, that dandruff is linked to the balance between bacteria and fungi of the host scalp surface.
Computation of discontinous optical flow by domain decomposition and shape optimization

We introduce an approach for the identification and tracking of image regions in monocular image sequences. The assumptions are that the egomotion is known and that an representation of the environment has been computed in order to predict roughly the expected motion field with respect to the movement of the sensor relative to the environment. Image regions, whose motions do not match with this motion field, are assumed to belong to independently moving objects in the scene. Having detected roughly the location and movement of such a region in the image plane (by Optical Flow or any other approach), we decompose the image plane in two disjoint domains and alter their shape such that the velocity fields which are computed for both domains agree in an optimal way with our interpretation of the scene. By this method we reconstruct a velocity field for the whole domain of the image plane, which is discontinuous along a closed contour. This contour coincides in an optimal, just described way with the motion boundaries of the object. As a result, a segmentation of the velocity field a posteriori becomes superfluous.
Global mapping of infectious disease

The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.
A novel Hybrid Inaudible Audio Watermarking with Binary Image as Watermark using DWT

Digital audio watermarking has become an important technique for copyright protection and secured data communication. There are numerous algorithms evolving in audio watermarking. We propose a novel hybrid inaudible algorithm for watermarking audio signals using Discrete Wavelet Transform (DWT). In our proposed algorithm we are using audio signal as host information and binary image as watermark. The multi resolution properties of DWT properties like transpose, flip, rotation, scaling and translation invariance are making the watermarking process robust and more capacitive (to hold large amounts of information). Our spread spectrum based embedding algorithm is verified for various watermarking coefficients (α) and proposed to have to variable α according to quantization levels of host information instead of single value. Our proposed algorithm is tested for various types of music signals with varying bit rates as host information and binary image as watermark. The proposed algorithm is tested and found very robust to filtering, extra noise, resampling, quantization and MP3 compression attacks. In this paper we also compare the performance of our algorithm with existing DWT based, techniques in information capacity (PSNR) and robustness (Normalized Correlation Coefficient).
Modelling the Manifold of Facial Expression Using Texture

The speed and intensity of the appearance changes that occur during the formation of facial expressions provide important information about the underlying meaning of the expression itself. In the past we have demonstrated the effectiveness of using locally linear embedding with facial shape information for estimating the dynamics of facial expression. This approach was only suitable for specific expressions, where the appearance change was principally due to a movement or distortion of the shape of facial features. However, for some facial expressions, the variation in the shape of the facial features is very subtle. These expressions are mainly characterised by the variation in the texture of the face. Hence such expressions are not amenable to the previous approach. In order to estimate the dynamics of these types of expressions it is necessary to develop nonlinear appearance models that incorporate texture information. In this paper we use LLE to estimate the manifold of texture variation due to facial expression. We show that the resulting manifold effectively captures the underlying dynamics of facial expression and that it provides a suitable representation for differentiation between posed and spontaneous expressions.
Design and Performance Evaluation of Channel Reservation Schemes for QoS Constrained Multimedia Traffic

This paper considers the problem of contension resolution problems for high bit-rate wireless communication systems where the round trip propagation delay is relatively longer than the slot transmission time. In this scenario, we found that existing channel reservation schemes cannot guarantee the satisfaction to all users regarding different quality of service (QoS). Thus in this paper, we propose 2 new channel reservation schemes which taken into consideration priority service to more delay-sensitive multimedia traffics, namely, Partial UNI and UNI+MT schemes for multimedia traffics, an extension of our recently proposed UNI scheme for single-class traffic. The goal is to achieve the highest system performance and enable each traffic types to meet their QoS requirements. We evaluate the performance of each scheme by mathematical analysis. The numerical results show that our proposed schemes are effective in enabling different traffic users to achieve the best successful rate possible in this kind of environment.
The Structure of Insulin

It is curious to read once again the text of the paper by Dr. Moses Barron1 which was first read by Fred Banting on October 30, 1920, and which stirred him so urgently to attempt the isolation of insulin. He stopped at the library casually on the way home from the medical school and looked at the first paper in Surgery, Gynecology and Obstetrics. Because he had to talk to students on the following day on the function of the pancreas and because its title was “The relation of the islets of Langerhans to Diabetes with special reference to cases of Pancreatic Lithiasis,” he took the journal home with him. The sentences he underlined were “Arnozan and Vaillard ligated the pancreatic ducts in rabbits and found that within twenty-four hours the ducts became dilated, the epithelial cells were desquamated and there were protoplasmic changes in the acinic cells … Ssobolew ligated the ducts in rabbits, cats and dogs. He found a gradual atrophy and sclerosis of the organ and relatively intact islets and no glycosuria. ” At 9 p.m. Banting rang up Dr. Tew to say that he had an idea-that it might be possible to isolate the antidiabetic hormone from the islets by first allowing the acinar cells, containing digestive ferments, to atrophy. It was an idea so powerful that it changed his life and the lives of manv others.