Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing microRNA screening as a functional genomics tool for disease research

Originally discovered as regulators of developmental timing in C. elegans, microRNAs (miRNAs) have emerged as modulators of nearly every cellular process, from normal development to pathogenesis. With the advent of whole genome libraries of miRNA mimics suitable for high throughput screening, it is possible to comprehensively evaluate the function of each member of the miRNAome in cell-based assays. Since the relatively few microRNAs in the genome are thought to directly regulate a large portion of the proteome, miRNAome screening, coupled with the identification of the regulated proteins, might be a powerful new approach to gaining insight into complex biological processes.
Assessing the vulnerability of network topologies under large-scale regional failures

Natural disasters often lead to regional failures that can cause network nodes and links co-located in a large geographical area to fail. Novel approaches are required to assess the network vulnerability under such regional failures. In this paper, we investigate the vulnerability of networks by considering the geometric properties of regional failures and network nodes. To evaluate the criticality of node locations and determine the critical areas in a network, we propose the concept of α-critical-distance with a given failure impact ratio α, and we formulate two optimization problems based on the concept. By analyzing the geometric properties of the problems, we show that although finding critical nodes or links in a pure graph is a NP-complete problem, the problem of finding critical areas has polynomial time complexity. We propose two algorithms to deal with these problems and analyze their time complexities. Using real city-level Internet topology data, we conducted experiments to compute the α-critical-distances for different networks. The computational results demonstrate the differences in vulnerability of different networks. The results also indicate that the critical area of a network can be estimated by limiting failure centers on the locations of network nodes. Additionally, we find that with the same impact ratio α, the topologies examined have larger α-critical-distances when the network performance is measured using the giant component size instead of the other two metrics. Similar results are obtained when the network performance is measured using the average two terminal reliability and the network efficiency, although computation of the former entails less time complexity than that of the latter.
Effect of the addition of Psyllium fiber on wheat flour dough rheological properties

The aim of this work was to quantify the effects of psyllium fiber addition to wheat flour at the levels of 0, 1, 2, 3 and 4% on the rheological behavior of the dough. The rheological properties of the dough were investigated using the rheological device, Farinograph. Upon the addition of psyllium fiber, a significant increase in Farinograph water absorption, simultaneously with the increase of the addition level, was recorded. The psyllium fiber addition has the effect of increasing development time and stability upon to ≤ 2 %. Also, the degree of softening of the dough increased with the increase of the psyllium fiber upon at level of ≤ 3 %. Psyllium fiber added in wheat flour up to 4% increased the falling number (FN) index. Therefore, using psyllium fiber at an optimal level, allows an increase of the daily intake of fiber without promoting negative effects on the rheological properties of the dough.
The significance of micas in ancient cross-bedded sandstones

The cross-bedded Coconino Sandstone is almost certainly within the stratigraphic range of the Flood, however it is commonly cited by conventional geologists as the classic example of an eolian deposit, and thus an argument against the scientific viability of the Flood. In our petrographic study of the Coconino Sandstone, we discovered muscovite mica (and sometimes biotite mica) in almost every thin section. This is surprising given that micas have not previously been reported in this, or any, “eolian” cross-bedded deposit. The mica found is detrital in character (i.e., it is not an alteration product) and thus is part of the primary depositional fabric. This led to the investigation of other cross-bedded sandstones from around the world, especially those of similar stratigraphic age, all of which have been conventionally interpreted as wholly or partly eolian– the same frequent occurrence of micas was observed. Previous laboratory experiments have provided some framework for understanding this discovery. Based on those experiments, it was found that mica cannot survive continuous transport much more than four days (or about 500 km) by simulated eolian processes, but can last for more than a year (or about 7,500 km) when transported continuously by simulated subaqueous processes. Field observations confirm that modern ergs contain virtually no micas, of any size, except in cases where mica sources (such as granite outcrops, beach sand or fluvial sand) are located in the immediate vicinity (~<10 km) of the erg. By contrast, the Coconino sand body and its correlative stratigraphic units stretch for many hundreds of kilometers across (with a total area of 2.4 million km2), and therefore the interior of the deposit should be virtually mica-free if formed by eolian processes. We catalog and illustrate a large number of cross-bedded sandstones that contain mica grains (mostly muscovite) as an accessory mineral. The dominant conventional view is that these sandstones are eolian in origin, but experimental data and field observations suggest otherwise. The presence of micas in cross-bedded sandstones is a previously neglected criterion that can be used to argue for a subaqueous depositional environment for the formation of cross-bedded sandstones.
Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5.

Section 5 of the Toxic Substances Control Act (TSCA) requires that manufacturers and importers of new chemicals must submit a Premanufacture Notification (PMN) to the U.S. Environmental Protection Agency 90 days before they intend to commence manufacture or import. Certain information such as chemical identity, uses, etc., must be included in the notification. The submission of test data on the new substance, however, is not required, although any available health and environmental information must be provided. Nonetheless, over half of all PMNs submitted to the agency do not contain any test data; because PMN chemicals are new, no test data is generally available in the scientific literature. Given this situation, EPA has had to develop techniques for hazard assessment that can be used in the presence of limited test data. EPA's approach has been termed "structure-activity relationships" (SAR) and involves three major components: the first is critical evaluation and interpretation of available toxicity data on the chemical; the second component involves evaluation of test data available on analogous substances and/or potential metabolites; and the third component involves the use of mathematical expressions for biological activity known as "quantitative structure-activity relationships" (QSARs). At present, the use of QSARs is limited to estimating physical chemical properties, environmental toxicity, and bioconcentration factors. An important overarching element in EPA's approach is the experience and judgment of scientific assessors in interpreting and integrating the available data and information. Examples are provided that illustrate EPA's approach to hazard assessment for PMN chemicals.
Empirical Evaluation and New Design for Fighting Evolving Twitter Spammers

To date, as one of the most popular online social networks (OSNs), Twitter is paying its dues as more and more spammers set their sights on this microblogging site. Twitter spammers can achieve their malicious goals such as sending spam, spreading malware, hosting botnet command and control (C&C) channels, and launching other underground illicit activities. Due to the significance and indispensability of detecting and suspending those spam accounts, many researchers along with the engineers at Twitter Inc. have devoted themselves to keeping Twitter as spam-free online communities. Most of the existing studies utilize machine learning techniques to detect Twitter spammers. “While the priest climbs a post, the devil climbs ten. ” Twitter spammers are evolving to evade existing detection features. In this paper, we first make a comprehensive and empirical analysis of the evasion tactics utilized by Twitter spammers. We further design several new detection features to detect more Twitter spammers. In addition, to deeply understand the effectiveness and difficulties of using machine learning features to detect spammers, we analyze the robustness of 24 detection features that are commonly utilized in the literature as well as our proposed ones. Through our experiments, we show that our new designed features are much more effective to be used to detect (even evasive) Twitter spammers. According to our evaluation, while keeping an even lower false positive rate, the detection rate using our new feature set is also significantly higher than that of existing work. To the best of our knowledge, this work is the first empirical study and evaluation of the effect of evasion tactics utilized by Twitter spammers and is a valuable supplement to this line of research.
Factors Controlling the Trafficking and Processing of a Leader-Derived Peptide Presented by Qa-11

Many leader-derived peptides require TAP for presentation by class I molecules. This TAP dependence can either be ascribed to the inability of proteases resident in the endoplasmic reticulum (ER) to trim leader peptide precursors into the appropriate epitope or the failure of a portion of the leader segment to gain access to the lumen of the ER. Using the Qa-1 binding epitope, Qdm derived from a class Ia leader as a model, we show that many cell types lack ER protease activity to trim this peptide at its C terminus. However, both T1 and T2 cells contain appropriate protease activity to process the full length Dd leader (DL) when introduced into the ER lumen. Nevertheless, both T1 cells treated with the TAP inhibitor ICP47 and TAP− T2 cells fail to present this epitope from either the intact Dd molecule or a minigene encoding the DL. This indicates that the portion of the leader containing Qdm does not gain access to the ER. However, changing the Arg at P7 of the DL to a Cys can alter its trafficking and allows for TAP-independent presentation of the Qdm epitope.
Network Approximation for Effective Viscosity of Concentrated Suspensions with Complex Geometry

We study suspensions of rigid particles (inclusions) in a viscous incompressible fluid. The particles are close to touching one another, so that the suspension is near the packing limit, and the flow at small Reynolds number is modeled by the Stokes equations. The objective is to determine the dependence of the effective viscosity � μ� on the geometric properties of the particle array. We study spatially irregular arrays, for which the volume fraction alone is not sufficient to estimate the effective viscosity. We use the notion of the interparticle distance parameter δ, based on the Voronoi tessellation, and we obtain a discrete network approximation of � μ� ,a sδ → 0. The asymptotic formulas for � μ� , derived in dimensions two and three, take into account translational and rotational motions of the particles. The leading term in the asymptotics is rigorously justified in two dimensions by constructing matching upper and lower variational bounds on � μ� . While the upper bound is obtained by patching together local approximate solutions, the construction of the lower bound cannot be obtained by a similar local analysis because the boundary conditions at fluid-solid interfaces must be resolved for all particles simultaneously. We observe that satisfying these boundary conditions, as well as the incompressibility condition, amounts to solving a certain algebraic system. The matrix of this system is determined by the total number of particles and their coordination numbers (number of neighbors of each particle). We show that the solvability of this system is determined by the properties of the network graph (which is uniquely defined by the array of particles) as well as by the conditions imposed at the external boundary.
Effectiveness of using an enterprise system to teach process-centered concepts in business education

This study investigates whether or not student’s performance, self‐efficacy, and satisfaction are enhanced by the use of an enterprise system as a support tool for learning business process and enterprise systems concepts. The study compares three instructional delivery methods. A traditional instruction method (lecture format plus reading/exercises) serves as the control. The second and third instructional methods are computer‐based methods. In the second method, students receive traditional lecture format with full access to hands‐on an enterprise system transaction exercise. In the third method, students receive traditional lecture format, but also have full access to simulated hands‐on an enterprise system via Web transaction exercises (i.e. ScreenCam movies). A statistically significant difference between‐instructional methods effect is found. Post hoc analysis showed that the simulated hands‐on instruction group’s performance score was significantly higher than that of the control group. There were no other statistically significant differences found, but practical considerations at this learning environment are discussed.
Efficient algorithms for predicting requests to Web servers

Internet traffic has grown significantly with the popularity of the Web. Consequently user perceived latency in retrieving Web pages has increased. Caching and prefetching at the client side, aided by hints from the server, are attempts at solving this problem. We suggest techniques to group resources that are likely to be accessed together into volumes, which are used to generate hints tailored to individual applications, such as prefetching, cache replacement, and cache validation. We discuss theoretical aspects of optimal volume construction, and develop efficient heuristics. Tunable parameters allow our algorithms to predict as many accesses as possible while reducing false predictions and limiting the size of hints. We analyze a collection of large server logs, extracting access patterns to construct and evaluate volumes. We examine sampling techniques to process only portions of the server logs while constructing equally good volumes. We show that it is possible to predict requests at low cost with a high degree of precision.
Absence of HHV-8 in prostate and semen.

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Quantitative measurement of paramyxovirus fusion: differences in requirements of glycoproteins between simian virus 5 and human parainfluenza virus 3 or Newcastle disease virus

To compare the requirements for paramyxovirus-mediated cell fusion, the fusion (F) and hemagglutinin-neuraminidase (HN) glycoproteins of simian virus 5 (SV5), human parainfluenza virus 3 (HPIV-3), and Newcastle disease virus (NDV) were expressed individually or coexpressed in either homologous or heterologous combinations in CV-1 or HeLa-T4 cells, using the vaccinia virus-T7 polymerase transient expression system. The contribution of individual glycoproteins in virus-induced membrane fusion was examined by using a quantitative assay for lipid mixing based on the relief of self-quenching (dequenching) of fluorescence of the lipid probe octadecyl rhodamine (R18) and a quantitative assay for content mixing based on the cytoplasmic activation of a reporter gene, beta-galactosidase. In these assays, expression of the individual F glycoproteins did not induce significant levels of cell fusion and no cell fusion was observed in experiments when cells individually expressing homologous F or HN proteins were mixed. However, coexpression of homologous F and HN glycoproteins resulted in extensive cell fusion. The kinetics of fusion were found to be very similar for all three paramyxoviruses studied. With NDV and HPIV-3, no cell fusion was detected when F proteins were coexpressed with heterologous HN proteins or influenza virus hemagglutinin (HA). In contrast, SV5 F protein exhibited a considerable degree of fusion activity when coexpressed with either NDV or HPIV-3 HN or with influenza virus HA, although the kinetics of fusion were two- to threefold higher when the homologous SV5 F and HN proteins were coexpressed. Thus, these data indicate that among the paramyxoviruses tested, SV5 has different requirements for cell fusion.
Clues to the nature of high-redshift O vi absorption systems from their lack of small-scale structure

We present results of the first survey of high-redshift $(\langle z\rangle\sim 2.3)$ $\ion{O}{vi}$ absorption systems along parallel lines of sight toward two lensed QSOs. After a careful and well-defined search, we find ten intervening $\ion{O}{vi}$ systems – identified by the presence of the $\lambda\lambda$1031, 1037 doublet lines, $\ion{H}{i}$, and in most cases $\ion{C}{iv}$, $\ion{Si}{iv}$, and $\ion{C}{iii}$ – and eight candidate systems for which we do not detect $\ion{H}{i}$ nor other metals. We assess the veracity of these systems by applying a classification scheme. Within the errors, all $\ion{O}{vi}$ systems appear at the same redshift and have similar line strengths in front of both QSO images, whereas in most cases $\ion{C}{iv}$ or $\ion{Si}{iv}$ show more differences across the lines of sight, either in radial velocity or line strength. We conclude that (1) the coherence length of $\ion{O}{vi}$ must be much larger than $\approx $1 $h_{70}^{-1}$ kpc, and (2) an important fraction of the $\ion{C}{iv}$ absorbers may not reside in the same volume as $\ion{O}{vi}$. Given the inhomogeneous character of the data – different $S/N$ ratios and degrees of blending – we pay special attention to the observational errors and their impact on the above conclusions. Since Doppler parameters are consistent with photoionization, we propose a model in which $\ion{C}{iv}$ occurs in two different photoionized phases, one large, with characteristic sizes of a few hundred kpc and bearing $\ion{O}{vi}$, and another one a factor of ten smaller and containing $\ion{C}{iii}$. This model is able to explain the various transverse differences observed in column density and kinematics. We apply the model successfully to 2 kinds of absorbers, with low and high metallicity. In the low-metallicity regime, [C/H]~ -2, we find that [C/O] ≈ -0.7 is required to explain the observations, which hints at late ($z\la 6$) rather than early metal enrichment. In the high-metallicity regime, the observed dissociation between $\ion{O}{vi}$ and $\ion{C}{iv}$ gas might be produced by galactic outflows. Altogether, the relative abundances, inhomogeneous $\ion{C}{iv}$ and featureless $\ion{O}{vi}$ are consistent with gas that has been processed recently before the absorption occurred (thus close to star-forming regions). Finally, we discuss briefly three associated systems $(z_{\rm abs} \sim z_{\rm em})$ that also show $\ion{O}{vi}$.
A Variance Reduced Stochastic Newton Method

Quasi-Newton methods are widely used in practise for convex loss minimization problems. These methods exhibit good empirical performance on a wide variety of tasks and enjoy super-linear convergence to the optimal solution. For large-scale learning problems, stochastic Quasi-Newton methods have been recently proposed. However, these typically only achieve sub-linear convergence rates and have not been shown to consistently perform well in practice since noisy Hessian approximations can exacerbate the effect of high-variance stochastic gradient estimates. In this work we propose Vite, a novel stochastic Quasi-Newton algorithm that uses an existing first-order technique to reduce this variance. Without exploiting the specific form of the approximate Hessian, we show that Vite reaches the optimum at a geometric rate with a constant step-size when dealing with smooth strongly convex functions. Empirically, we demonstrate improvements over existing stochastic Quasi-Newton and variance reduced stochastic gradient methods.
6/2/06 Perioperative Assessment of the Cardiovascular System in ESLD and Transplantation

The liver transplant procedure poses a significant stress on the heart: there are major changes in preload due to clamping and unclamping of major vessels and bleeding; contractility can be affected by ionized hypocalcemia, major acid-base abnormalities, and substances released from the reperfused graft; and afterload, already low at baseline, can decrease dramatically after graft reperfusion. All of these can result in severe hypotension, which might not be tolerated by the diseased heart. Alternatively, cardiac pathology can result in more severe hemodynamic instability during the liver transplant procedure, because the diseased heart has less reserve and therefore does not tolerate the changes in preload, contractility, and afterload as well. This may jeopardize the perfusion and consequently the function of the new graft and possibly other essential organs, including the heart itself. Therefore, it is imperative to do a thorough evaluation of the cardiovascular system preoperatively, and to appropriately monitor the cardiovascular system intra and postoperatively. It may be necessary to intervene preoperatively (eg, coronary stent placement) or to do combined surgery [eg, combined coronary artery bypass grafting (CABG) and liver transplantation]. Patients with poor cardiac function (eg, left ventricular ejection fraction <35%) or patients whose cardiac condition cannot be improved significantly may not be appropriate candidates for liver transplantation (LTx). Finally, vascular abnormalities that may occur in liver disease, such as superior vena cava syndrome, migrated transjugular intrahepatic portosystemic shunt (TIPS) cannula, or significant carotid artery disease has to be recognized before starting the liver transplant procedure. In this chapter, we will first discuss the cardiovascular pathophysiology in end-stage liver disease (ESLD), and then we will present the evaluation, monitoring, and optimization/management of the cardiovascular system before and during the liver transplant procedure.