Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence-Specific Inhibition of Small RNA Function

Hundreds of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) have been identified from both plants and animals, yet little is known about their biochemical modes of action or biological functions. Here we report that 2′-O-methyl oligonucleotides can act as irreversible, stoichiometric inhibitors of small RNA function. We show that a 2′-O-methyl oligonucleotide complementary to an siRNA can block mRNA cleavage in Drosophila embryo lysates and HeLa cell S100 extracts and in cultured human HeLa cells. In Caenorhabditis elegans, injection of the 2′-O-methyl oligonucleotide complementary to the miRNA let-7 can induce a let-7 loss-of-function phenocopy. Using an immobilized 2′-O-methyl oligonucleotide, we show that the C. elegans Argonaute proteins ALG-1 and ALG-2, which were previously implicated in let-7 function through genetic studies, are constituents of a let-7-containing protein–RNA complex. Thus, we demonstrate that 2′-O-methyl RNA oligonucleotides can provide an efficient and straightforward way to block small RNA function in vivo and furthermore can be used to identify small RNA-associated proteins that mediate RNA silencing pathways.
Mammalian target of rapamycin (mTOR): a central regulator of male fertility?

Abstract Mammalian target of rapamycin (mTOR) is a central regulator of cellular metabolic phenotype and is involved in virtually all aspects of cellular function. It integrates not only nutrient and energy-sensing pathways but also actin cytoskeleton organization, in response to environmental cues including growth factors and cellular energy levels. These events are pivotal for spermatogenesis and determine the reproductive potential of males. Yet, the molecular mechanisms by which mTOR signaling acts in male reproductive system remain a matter of debate. Here, we review the current knowledge on physiological and molecular events mediated by mTOR in testis and testicular cells. In recent years, mTOR inhibition has been explored as a prime strategy to develop novel therapeutic approaches to treat cancer, cardiovascular disease, autoimmunity, and metabolic disorders. However, the physiological consequences of mTOR dysregulation and inhibition to male reproductive potential are still not fully understood. Compelling evidence suggests that mTOR is an arising regulator of male fertility and better understanding of this atypical protein kinase coordinated action in testis will provide insightful information concerning its biological significance in other tissues/organs. We also discuss why a new generation of mTOR inhibitors aiming to be used in clinical practice may also need to include an integrative view on the effects in male reproductive system.
Tumor Necrosis Factor Receptor–associated Factor 6 (TRAF6) Stimulates Extracellular Signal–regulated Kinase (ERK) Activity in CD40 Signaling Along a Ras-independent Pathway

CD40 activates nuclear factor kappa B (NFκB) and the mitogen-activated protein kinase (MAPK) subfamily, including extracellular signal–regulated kinase (ERK). The CD40 cytoplasmic tail interacts with tumor necrosis factor receptor–associated factor (TRAF)2, TRAF3, TRAF5, and TRAF6. These TRAF proteins, with the exception of TRAF3, are required for NFκB activation. Here we report that transient expression of TRAF6 stimulated both ERK and NFκB activity in the 293 cell line. Coexpression of the dominant-negative H-Ras did not affect TRAF6-mediated ERK activity, suggesting that TRAF6 may activate ERK along a Ras-independent pathway. The deletion mutant of TRAF6 lacking the NH2-terminal domain acted as a dominant-negative mutant to suppress ERK activation by full-length CD40 and suppress prominently ERK activation by a deletion mutant of CD40 only containing the binding site for TRAF6 in the cytoplasmic tail (CD40Δ246). Transient expression of the dominant-negative H-Ras significantly suppressed ERK activation by full-length CD40, but marginally suppressed ERK activation by CD40Δ246, compatible with the possibility that TRAF6 is a major transducer of ERK activation by CD40Δ246, whose activity is mediated by a Ras-independent pathway. These results suggest that CD40 activates ERK by both a Ras-dependent pathway and a Ras-independent pathway in which TRAF6 could be involved.
Immunoglobulin E and G4 antibodies in cysticercosis

The importance of immunoglobulin G (IgG) subclass responses in different infections has been elucidated for a number of organisms, but few parasitic organisms have been examined in this regard. In the current study, quantitative radioimmunoassays were used to examine the IgE and IgG4 subclass responses to larval Taenia solium. Patients were divided into clinically infected (CI) and probably uninfected (PU) groups. Unexposed normal subjects were used as controls. The CI group had elevated geometric mean levels of total IgE in serum (28.6 IU/ml) and specific IgG4 antibodies (438.8 arbitrary units [AU]/ml) compared with controls (8.3 IU/ml and 50.1 AU/ml, respectively). The CI group also had significantly elevated levels in cerebrospinal fluid of total IgG4 (18.6 micrograms/ml) and specific IgG4 antibodies (86.0 AU/ml) compared with the PU group (2.5 micrograms/ml and 1.6 AU/ml, respectively). There was no specific IgE antibody response detected in either the CI or PU patient group. The marked IgG4 response of CI patients to T. solium merits further investigation.
Reasoning about code mobility with mobile UNITY

Advancements in network technology have led to the emergence of new computing paradigms that challenge established programming practices by employing weak forms of consistency and dynamic forms of binding. Code mobility, for instance, allows for invocation-time binding between a code fragment and the location where it executes. Similarly, mobile computing allows hosts (and the software they execute) to alter their physical location. Despite apparent similarities, the two paradigms are distinct in their treatment of location and movement. This paper seeks to uncover a common foundation for the two paradigms by exploring the manner in which stereotypical forms of code mobility can be expressed in a programming notation developed for mobile computing. Several solutions to a distributed simulation problem are used to illustrate the modeling strategy and the ability to construct assertional-style proofs for programs that employ code mobility.
Generative representations for artificial architecture and passive solar performance

This paper explores how the use of generative representations influences the quality of solutions in evolutionary design problems. A genetic programming system is developed with individuals encoded as generative representations. Two research goals motivate this work. One goal is to examine Hornby's features and measures of modularity, reuse and hierarchy in new and more complex evolutionary design problems. In particular, we consider a more difficult problem domain where the generated 3D models are no longer constrained by voxels. Experiments are carried out to generate 3D models which grow towards a set of target points. The results show that the generative representations with the three features of modularity, regularity and hierarchy performed best overall. Although the measures of these features were largely consistent with those of Hornby, a few differences were found. Our second research goal is to use the best performing encoding on some 3D modeling problems that involve passive solar performance criteria. Here, the system is challenged with generating forms that optimize exposure to the Sun. This is complicated by the fact that a model's structure can interfere with solar exposure to itself; for example, protrusions can block Sun exposure to other model elements. Furthermore, external environmental factors (geographic location, time of the day, time of the year, other buildings in the proximity) may also be relevant. Experimental results were successful, and the system was shown to scale well to the architectural problems studied.
Changes in Synaptic Transmission and Long-term Potentiation Induction as a Possible Mechanism for Learning Disability in an Animal Model of Multiple Sclerosis

Purpose: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system. It has been shown that memory deficits is common in patients with MS. Recent studies using experimental autoimmune encephalomyelitis (EAE) as an animal model of MS have shown that indicated that EAE causes hippocampal-dependent impairment in learning and memory. Thus far, there have been no in vivo electrophysiological reports describing synaptic transmission in EAE animals. The aim of the present work is to evaluate the synaptic changes in the CA1 region of the hippocampus of EAE rats. Methods: To evaluate changes in synaptic transmission in the CA1 region of the hippocampus of EAE rats, field excitatory postsynaptic potentials (fEPSPs) from the stratum radiatum of CA1 neurons, were recorded following Schaffer collateral stimulation. Results: The results showed that EAE causes deficits in synaptic transmission and long-term potentiation (LTP) in the hippocampus. In addition, paired-pulse index with a 120 msec interstimulus interval was decreased in the EAE group. These findings indicate that EAE might induce suppression in synaptic transmission and LTP by increasing the inhibitory effect of GABAB receptors on the glutamate-mediated EPSP. Conclusions: In conclusion, influence of inflammation-triggered mechanisms on synaptic transmission may explain the negative effect of EAE on learning abilities in rats.
Approximating minimum size weakly-connected dominating sets for clustering mobile ad hoc networks

We present a series of approximation algorithms for finding a smallweakly-connected dominating set (WCDS) in a given graph to be usedin clustering mobile ad hoc networks. The structure of a graph canbe simplified using WCDS's and made more succinct for routing in adhoc networks. The theoretical performance ratio of these algorithmsis O(ln Δ) compared to the minimum size WCDS, whereΔ is the maximum degree of the input graph. The first twoalgorithms are based on the centralized approximation algorithms ofGuha and Khuller cite guha-khuller-1998 for finding small connecteddominating sets (CDS's). The main contribution of this work is acompletely distributed algorithm for finding small WCDS's and theperformance of this algorithm is shown to be very close to that ofthe centralized approach. Comparisons between our work and someprevious work (CDS-based) are also given in terms of the size ofresultant dominating sets and graph connectivity degradation.
Amelioration of Cancer Stem Cells in Macrophage Colony Stimulating Factor-Expressing U87MG-Human Glioblastoma upon 5-Fluorouracil Therapy

Macrophage colony stimulating factor (MCSF) regulates growth, proliferation and differentiation of haematopoietic cell lineages. Many cancers are known to secrete high level of MCSF, which recruit macrophages into the tumour micro-environment, supporting tumour growth. Herein, we report the cloning of MCSF and subsequent generation of U87MG expressing MCSF stable cell line (U87-MCSF). Cytotoxicity of anti-cancer drug 5-fluorouracil (5-FU) was evaluated on both U87MG and U87-MCSF cells. Interestingly, the proliferation of U87-MCSF cells was less (p<0.001) than that of U87MG cells alone, after treatment with 5-FU. Significant decrease in expression levels of cyclin E and A2 quantified by real time PCR analysis corroborated the reduced proliferation of 5-FU treated U87-MCSF cells. However, JC-1 staining did not reveal any apoptosis upon 5-FU treatment. Notch-1 upregulation induced a possible epithelial-mesenchymal transition in U87-MCSF cells, which accounted for an increase in the proportion of CD24high/CD44less cancer stem cells in U87-MCSF cells after 5-FU treatment. The elevated resistance of U87-MCSF cells towards 5-FU was due to the increase in the expressions (10.2 and 6 fold) of ABCB1 and mdm2, respectively. Furthermore, increase in expressions of ABCG1, mdm2 and CD24 was also observed in U87MG cells after prolonged incubation with 5-FU. Our studies provided mechanistic insights into drug resistance of U87MG cells and also described the pivotal role played by MCSF in augmenting the resistance of U87MG cells to 5-FU.
A limit process for partial match queries in random quadtrees

We consider the problem of recovering items matching a partially specified pattern in multidimensional trees (quadtrees and k-d trees). We assume the classical model where the data consist of independent and uniform points in the unit square. For this model, in a structure on $n$ points, it is known that the complexity, measured as the number of nodes $C_n(\xi)$ to visit in order to report the items matching a random query $\xi$, independent and uniformly distributed on $[0,1]$, satisfies $E{C_n(\xi)}\sim \kappa n^{\beta}$, where $\kappa$ and $\beta$ are explicit constants. We develop an approach based on the analysis of the cost $C_n(s)$ of any fixed query $s\in [0,1]$, and give precise estimates for the variance and limit distribution. Moreover, a functional limit law for a rescaled version of the process $(C_n(s))_{0\le s\le 1}$ is derived in the space of c\'{a}dl\'{a}g functions with the Skorokhod topology. For the worst case complexity $\max_{s\in [0,1]} C_n(s)$ the order of the expectation as well as a limit law are given.
Auditory Verbal Hallucinations: can Beliefs about Voices Mediate the Relationship Patients establish with them and Negative Affect?

Abstract This study was designed to find out whether a person’s relationship with his voices and the negative affect he suffers from are mediated by beliefs about the voices. Research done to date shows contradictory results (Sorrell, Hayward, & Meddings, 2010, Vaughan & Fowler, 2004). A cross-sectional study was done to study the associations among variables, and a multiple mediation model (Preacher & Hayes, 2008) in which the beliefs about voices were the mediating variables was tested. Sixty subjects who heard voices participated. The VAY (Hayward, Denney, Vaughan, & Fowler, 2008), BAVQ (Chadwick & Birchwood, 1995), BAI (Beck & Steer, 1993) and BDI-II (Beck, Steer & Brown, 1996) were given. We found a significant positive correlation between perception of voices as dominant and intrusive and maintaining a position of distance from them on one hand, and negative affect [anxiety (r = .57, p < .001; r = .40, p < .001; r = .34, p < .01 respectively) and depression (r = .58, p < .001; r = .37, p < .01; r = .38, p < .001 respectively)] on the other. We also found that beliefs of malevolence and omnipotence mediated between relating style and negative affect (anxiety and depression). The theoretical implications of the results and clinical implications of the mediating relationships found are discussed.
Mixing across a density interface in a Taylor-Couette flow

In this paper we report on an experimental investigation of the interfacial mixing by Taylor vortices. Using the LIF method the evolution of the density field is followed in time for a range of buoyancy frequencies and Reynolds numbers. It is found that the buoyancy flux, represented as a function of the buoyancy gradient, shows a similar tendency as the mixing in isotropic turbulent flows. New is the increase in buoyancy flux for very large buoyancy gradients, predicted by the model of Balmforth et al. (1998). Since shear instabilities are unlikely to occur, other changes in the mixing processes should be responsible. In addition a spread in the maximum mixing efficiency is found, which is dependent on Reynolds number. The origins of this Reynolds number dependence, as well as the application of the mixing results to Langmuir Circulation in the ocean thermocline are discussed.
Automatic generation of high-performance trace compressors

Program execution traces are frequently used in industry and academia. Yet, most trace-compression algorithms have to be re-implemented every time the trace format is changed, which takes time, is error prone, and often results in inefficient solutions. This paper describes and evaluates TCgen, a too that automatically generates portable, customized, high-performance trace compressors. All the user has to do is provide a description of the trace format and select one or more predictors to compress the fields in the trace records. TCgen translates this specification into C source code and optimizes it for the specified trace format and predictor algorithms. On average, the generated code is faster and compresses better than the six other compression algorithms we have tested. For example, a comparison with SBC, one of the best trace-compression algorithms in the current literature, shows that TCgen's synthesized code compresses SPECcpu2000 address traces 23% more, decompresses them 24% faster, and compresses them 1029% faster.
A new self-adapt DCF algorithm

This paper has first presented an in-depth analysis on the distributed coordination function (DCF) access mode of IEEE802.11 protocol. Based on the result of our study, we have concluded a new self-adapt wireless LAN MAC algorithm. Numerous simulation results have shown that the new algorithm can achieve the self-adapt character with the growing of node number and is superior to the original DCF algorithm in the characters concerned (e.g. throughput, fairness).
How speaker tongue and name source language affect the automatic recognition of spoken names

In this paper the automatic recognition of person names and geographical names uttered by native and non-native speakers is examined in an experimental set-up. The major aim was to raise our understanding of how well and under which circumstances previously proposed methods of multilingual pronunciation modeling and multilingual acoustic modeling contribute to a better name recognition in a cross-lingual context. To come to a meaningful interpretation of results we have categorized each language according to the amount of exposure a native speaker is expected to have had to this language. After having interpreted our results we have also tried to find an answer to the question of how much further improvement one might be able to attain with a more advanced pronunciation modeling technique which we plan to develop.
Uncertainty of the Linear Trend in the Zonal SST Gradient Across the Equatorial Pacific Since 1881

ABSTRACT The change in the zonal sea surface temperature gradient (ZSSTG) across the equatorial Pacific plays an important role in the global climate system. However, there has not yet been a consensual conclusion about the changing ZSSTG at either a short-term (from 20 to 90 years) or a long-term time scale (longer than 90 years) in the literature. In this study, the uncertainty of the trend in ZSSTG for different sub-periods since 1881 was examined using four interpolated datasets and four un-interpolated datasets. It was found that the trend in ZSSTG on the short-term time scale could be significantly influenced by internal variability such as the El Niño–Southern Oscillation and the Pacific Decadal Oscillation. On the long-term time scale, the sign of the ZSSTG trend depends on the dataset used. In particular, it was not possible to draw a uniform conclusion about the secular trends in ZSSTG in recent history, given the high sensitivity of the ZSSTG trends to the period, dataset, and regions used to calculate the trends. Our results imply that it may not be possible to detect the response of ZSSTG to global warming until a longer data record becomes available in the future.
GiST scan acceleration using coprocessors

Efficient lookups in huge, possibly multi-dimensional datasets are crucial for the performance of numerous use cases that generate multiple search operations at the same time, like point queries in ray tracing or spatial joins in collision detection of interactive 3D applications. These applications greatly benefit from index structures that quickly filter relevant candidates for further processing. Since different lookup operations are independent from each other, they might be processed in parallel on modern hardware like multi-core CPUs or GPUs. But implementing efficient algorithms for all kinds of indexes on various hardware platforms is a challenging task. In this paper, we present a new approach that extends the existing GiST index framework with an abstraction layer for the hardware where index operations are executed. Furthermore, we provide first performance evaluations for the scan execution on CPUs and an Nvidia Tesla GPU.
Procedure for assessing the reliability of prosodic judgements using sp-TOBI labeling system

This paper reports on the results of a pilot study that was run to assess the labeling consistency of the proposed approach in Sp-ToBI before starting a large-scale production of annotations in the project Glissando. This test should serve to refine the model and to maintain consistently the annotation conventions across transcription sites. The Spanish ToBI labeling system has been proved as an effective system to annotate intonation for Spanish, although the annotation conventions across transcribers require a broader consensus. This is specially needed in the following pitch accents: high pitch accent (H*) vs rising pitch accent (L+H*), downstepped pitch accents versus nondownstepped counterparts, and mid tones. A related issue is the difficulty to decide in a very low pitch range if a tone is present or if the syllable has been unaccented. Moreover, the statistical procedures will shed light on the most confusable tones suggesting new approaches for the automatic prediction of ToBI labels in a Spanish Spoken corpus.
Garp for kids: On the development of rational choice behavior

In this paper we examine the extent to which consumption choices by 7 and 11-year-old children and college undergraduates satisfy the axioms of revealed preference. We find that choices by even the 7-year-olds are considerably more likely to obey revealed preference axioms than would be true if they were choosing randomly. 11-year-olds do better still, while college students do no better than 11-year-old children. We also find that mathematical ability is not correlated with choosing rationally. We argue that this evidence suggests that the ability to choose rationally is not innate, but that it does develop quickly.
Nonlinear Amplifier Distortion in Cooperative Amplify-and-Forward OFDM Systems

This paper studies receiver techniques for nonlinear amplifier distortion compensation in an OFDM relay-assisted cooperative communication system. The system model includes a nonlinear amplifier at the amplify-and-forward relay, modeled as a solid state power amplifier (SSPA). A maximum ratio combiner (MRC) is introduced that includes the effects of the amplifier distortions. The MRC is obtained by a proper modeling of the nonlinear distortion noise. Furthermore, we introduce a power amplifier nonlinearity cancellation (PANC) technique that is suitable for cooperative systems. Our simulation results confirm that the new MRC and PANC techniques offer substantial performance improvements if the relayed signal is subject to nonlinear distortion.