Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular‐Regulated Kinases and Phosphatidylinositol 3‐Kinase Are Involved in Brain‐Derived Neurotrophic Factor‐Mediated Survival and neuritogenesis of the Neuroblastoma Cell Line SH‐SY5Y

Abstract : Retinoic acid (RA) induces the differentiation of many cell lines, including those derived from neuroblastoma. RA treatment of SH‐SY5Y cells induces the appearance of functional Trk B and Trk C receptors. Acute stimulation of RA‐predifferentiated SH‐SY5Y cells with brain‐derived neurotrophic factor (BDNF), neurotrophin 3 (NT‐3), or neurotrophin 4/5 (NT‐4/5), but not nerve growth factor (NGF), induces Trk autophosphorylation, followed by phosphorylation of Akt and the extracellular signal‐regulated kinases (ERKs) 1 and 2. In addition, BDNF, NT‐3, or NT‐4/5, but not NGF, promotes cell survival and neurite outgrowth in serum‐free medium. The mitogen‐activated protein kinase and ERK kinase (MEK) inhibitor PD98059 blocks BDNF‐induced neurite outgrowth and growth‐associated protein‐43 expression but has no effects on cell survival. On the other hand, the phosphatidylinositol 3‐kinase inhibitor LY249002 reverses the survival response elicited by BDNF, leading to a cell death with morphological features of apoptosis.
A Novel Proteomic Screen for Peptide-Protein Interactions*

Regulated interactions between short, unstructured amino acid sequences and modular protein domains are central to cell signaling. Here we use synthetic peptides in “active” (e.g. phosphorylated) and “control” (e.g. non-phosphorylated) forms as baits in affinity pull-down experiments to determine such interactions by quantitative proteomics. Stable isotope labeling by amino acids in cell culture distinguishes specific binders directly by the isotope ratios determined by mass spectrometry (Blagoev, B., Kratchmarova, I., Ong, S.-E., Nielsen, M., Foster, L. J., and Mann, M. (2003) Nat. Biotechnol. 21, 315–318). A tyrosine-phosphorylated peptide of the epidermal growth factor receptor specifically retrieved the Src homology domain (SH) 2- and SH3 domain-containing adapter protein Grb2. A proline-rich sequence of Son of Sevenless also specifically bound Grb2, demonstrating that the screen maintains specificity with low affinity interactions. The proline-rich Sos peptide retrieved only SH3 domain containing proteins as specific binding partners. Two of these, Pacsin 3 and Sorting Nexin 9, were confirmed by immunoprecipitation. Our data are consistent with a change in the role of Sos from Ras-dependent signaling to actin remodeling/endocytic signaling events by a proline-SH3 domain switch.
NOMA: Principles and recent results

Although non-orthogonal multiple access (NOMA) is recently considered for cellular systems, its key ideas such as successive interference cancellation (SIC) and superposition coding have been well studied in information theory. In this paper, we overview principles of NOMA based on information theory and present some recent results. Under a single-cell environment, we mainly focus on fundamental issues, e.g., power allocation and beamforming for downlink NOMA and coordinated and uncoordinated transmissions for uplink NOMA.
Integrating vision and audition within a cognitive architecture to track conversations

We describe a computational cognitive architecture for robots which we call ACT-R/E (ACT-R/Embodied). ACT-R/E is based on ACT-R [1, 2] but uses different visual, auditory, and movement modules. We describe a model that uses ACT-R/E to integrate visual and auditory information to perform conversation tracking in a dynamic environment. We also performed an empirical evaluation study which shows that people see our conversational tracking system as extremely natural.
Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening

Poor performance of scoring functions is a well-known bottleneck in structure-based virtual screening (VS), which is most frequently manifested in the scoring functions' inability to discriminate between true ligands vs known nonbinders (therefore designated as binding decoys). This deficiency leads to a large number of false positive hits resulting from VS. We have hypothesized that filtering out or penalizing docking poses recognized as non-native (i.e., pose decoys) should improve the performance of VS in terms of improved identification of true binders. Using several concepts from the field of cheminformatics, we have developed a novel approach to identifying pose decoys from an ensemble of poses generated by computational docking procedures. We demonstrate that the use of target-specific pose (scoring) filter in combination with a physical force field-based scoring function (MedusaScore) leads to significant improvement of hit rates in VS studies for 12 of the 13 benchmark sets from the clustered version of the Database of Useful Decoys (DUD). This new hybrid scoring function outperforms several conventional structure-based scoring functions, including XSCORE::HMSCORE, ChemScore, PLP, and Chemgauss3, in 6 out of 13 data sets at early stage of VS (up 1% decoys of the screening database). We compare our hybrid method with several novel VS methods that were recently reported to have good performances on the same DUD data sets. We find that the retrieved ligands using our method are chemically more diverse in comparison with two ligand-based methods (FieldScreen and FLAP::LBX). We also compare our method with FLAP::RBLB, a high-performance VS method that also utilizes both the receptor and the cognate ligand structures. Interestingly, we find that the top ligands retrieved using our method are highly complementary to those retrieved using FLAP::RBLB, hinting effective directions for best VS applications. We suggest that this integrative VS approach combining cheminformatics and molecular mechanics methodologies may be applied to a broad variety of protein targets to improve the outcome of structure-based drug discovery studies.
Improved criteria and comparative genomics tool provide new insights into grass paleogenomics

In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.
Making novel proteins from pseudogenes

MOTIVATION Recently, we made synthetic proteins from non-coding DNA of Escherichia coli. Encouraged by this, we asked: can we artificially express pseudogenes into novel and functional proteins? What kind of structures would be generated? Would these proteins be stable? How would the organism respond to the artificial reactivation of pseudogenes? RESULTS To answer these questions, we studied 16 full-length protein equivalents of pseudogenes. The sequence-based predictions indicated interesting molecular and cellular functional roles for pseudogene-derived proteins. Most of the proteins were predicted to be involved in the amino acid biosynthesis, energy metabolism, purines and pyrimidine biosynthesis, central intermediary metabolism, transport and binding. Interestingly, many of the pseudogene-derived proteins were predicted to be enzymes. Furthermore, proteins showed strong evidence of stable tertiary structures. The prediction scores for structure, function and stability were found to be favorable in most of the cases. IMPACT To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions.
BioNLP shared Task 2013 – An Overview of the Bacteria Biotope Task

This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2013, which follows BioNLP-ST-11. The Bacteria Biotope task aims to extract the location of bacteria from scientific web pages and to characterize these locations with respect to the OntoBiotope ontology. Bacteria locations are crucil knowledge in biology for phenotype studies. The paper details the corpus specifications, the evaluation metrics, and it summarizes and discusses the participant results.
234Th‐Derived Particle Fluxes and Seasonal Variability: When Is the SS Assumption Reliable? Insights From a Novel Approach for Carbon Flux Simulation

234Th measurements are widely used to estimate the downward carbon flux of particles via the oceanic Biological Pump. Carbon export is evaluated from 234Th‐238U disequilibrium assuming either steady state (SS) conditions, or including a non‐SS (NSS) correction. We use a novel stochastic simulation to quantify the temporal variation of vertical carbon and 234Th (dissolved and particulate) concentration profiles with high temporal resolution. We calculate seasonal export as if in situ measured with sediment trap and SS‐ and NSS‐234Th approaches and quantify the periods of validity for SS/NSS conditions defined in previous works. The SS approach is valid throughout the entire season in oligotrophic regions. In temperate regions, the SS introduces a bias in the export if sampling takes place outside specific temporal windows. Windows of validity range from days in short blooms of ~15‐day duration to weeks in blooms longer than ~30 days.
Upcall dispatcher aspects: combining modularity with efficiency in the CiAO IP stack

Network protocol stacks are an important ingredient of today's infrastructure software. For instance, all state-of-theart operating systems for PCs and the server market come with a TCP/IP stack. The design of protocol stacks and their layered structure has been studied for decades. However, in practice, implementations often do not follow the clean textbook design consequently. This especially holds for the domain of embedded TCP/IP stacks where minimal resource consumption is crucial. In this work we present an analysis that explains the reason for this dilemma. We have also developed a very simple solution that is based on common aspect-oriented programming language features: Upcall Dispatcher Aspects. In a case study this concept has been repeatedly applied as an AspectC++ idiom in the implementation of the CiAO TCP/IP stack, which we compared to several traditional implementations. Besides reecting a clean design at the implementation level, our protocol stack, which mainly targets the domain of resource-constrained embedded systems, even outperforms the other solutions with respect to resource consumption and various "-ilities"
Interlingual map task corpus collection

We present a prototype interlingual communication system that is being used to collect a corpus of task based dialogues between speakers of different languages. This corpus will be used to assess human reactions to an automated speech-to-speech translation system. In this demonstration we show how the HCRC Map Task can be adapted to support data collection in this interlingual environment, and how we used easily accessible speech and language technology for the rapid prototyping of the system used for data collection. An explanation of the nature and purpose of the data we are collecting is also presented.
The Same-Origin Attack against Location Privacy

A plethora of applications benefit from location context, but a person's whereabouts can be linked to her personal sensitive information. Hence, protection mechanisms have been proposed that add systematic noise to a user's location before sending it out of the user's device. We describe the same-origin attack, to which a group of such mechanisms are vulnerable, we evaluate it against two mechanisms (spatial cloaking and geo-indistinguishability), and we propose our own mechanism, inspired by the maximum entropy principle. We find that spatial cloaking is much worse than the other two, and the maximum-entropy mechanism performs slightly better than geo-indistinguishability. Designing an optimal mechanism remains an open problem.
CUNIT: A Semantic Role Labeling System for Modern Standard Arabic

In this paper, we present a system for Arabic semantic role labeling (SRL) based on SVMs and standard features. The system is evaluated on the released SEMEVAL 2007 development and test data. The results show an Fβ=1 score of 94.06 on argument boundary detection and an overall Fβ=1 score of 81.43 on the complete semantic role labeling task using gold parse trees.
An Almost Ideal Demand System

Ever since Richard Stone (1954) first estimated a system of demand equations derived explicitly from consumer theory, there has been a continuing search for alternative specifications and functional forms. Many models have been proposed, but perhaps the most important in current use, apart from the original linear expenditure system, are the Rotterdam model (see Henri Theil, 1965, 1976; Anton Barten) and the translog model (see Laurits Christensen, Dale Jorgenson, and Lawrence Lau; Jorgenson and Lau). Both of these models have been extensively estimated and have, in addition, been used to test the homogeneity and symmetry restrictions of demand theory. In this paper, we propose and estimate a new model which is of comparable generality to the Rotterdam and translog models but which has considerable advantages over both. Our model, which we call the Almost Ideal Demand System (AIDS), gives an arbitrary first-order approximation to any demand system; it satisfies the axioms of choice exactly; it aggregates perfectly over consumers without invoking parallel linear Engel curves; it has a functional form which is consistent with known household-budget data; it is simple to estimate, largely avoiding the need for non-linear estimation; and it can be used to test the restrictions of homogeneity and symmetry through linear restrictions on fixed parameters. Although many of these desirable properties are possessed by one or other of the Rotterdam or translog models, neither possesses all of them simultaneously. In Section I of the paper, we discuss the theoretical specification of the AIDS and justify the claims in the previous paragraph. In Section II, the model is estimated on postwar British data and we use our results to test the homogeneity and symmetry restrictions. Our results are consistent with earlier findings in that both sets of restrictions are decisively rejected. We also find that imposition of homogeneity generates positive serial correlation in the errors of those equations which reject the restrictions most strongly; this suggests that the now standard rejection of homogeneity in demand analysis may be due to insufficient attention to the dynamic aspects of consumer behavior. Finally, in Section III, we offer a summary and conclusions. We believe that the results of this paper suggest that the AIDS is to be recommended as a vehicle for testing, extending, and improving conventional demand analysis. This does not imply that the system, particularly in its simple static form, is to be regarded as a fully satisfactory explanation of consumers' behavior. Indeed, by proposing a demand system which is superior to its predecessors, we hope to be able to reveal more clearly the problems and potential solutions associated with the usual approach.
Design and Simulation of Low Noise Amplifier Circuit for 5 GHz to 6 GHz

— In first stage of each microwave receiver there is Low Noise Amplifier (LNA) circuit, and this stage has important rule in quality factor of the receiver. The design of a LNA in Radio Frequency (RF) circuit requires the trade-off many importance characteristics such as gain, Noise Figure (NF), stability, power consumption and complexity. This situation Forces desingners to make choices in the desing of RF circuits. In this paper the aim is to design and simulate a single stage LNA circuit with high gain and low noise using MESFET for frequency range of 5 GHz to 6 GHz. The desing simulation process is down using Advance Design System (ADS). A single stage LNA has successfully designed with 15.83 dB forward gain and 1.26 dB noise figure in frequency of 5.3 GHz. Also the designed LNA should be working stably In a frequency range of 5 GHz to 6 GHz.
Involvement of MAP Kinase in Angiotensin II-Induced Phosphorylation and Intracellular Targeting of Neuronal AT1 Receptors

MAP kinase stimulation is a key signaling event in the AT1 receptor (AT1R)-mediated chronic stimulation of tyrosine hydroxylase and norepinephrine transporter in brain neurons by angiotensin II (Ang II). In this study, we investigated the involvement of MAP kinase in AT1R phosphorylation to further our understanding of these persistent neuromodulatory actions of Ang II. Ang II caused a time-dependent phosphorylation of neuronal AT1R. This phosphorylation was associated with internalization and translocation of AT1R into the nucleus. MAP kinase also stimulated phosphorylation of neuronal AT1R. The conclusion that MAP kinase participates in neuronal AT1R phosphorylation and its targeting into the nucleus is supported further by the following. (1) MAP kinase-mediated phosphorylation of AT1R was blocked by the AT1R antagonist losartan; (2) AT1R co-immunoprecipitated with MAP kinase; (3) MAP kinase-kinase inhibitor PD98059 attenuated Ang II-induced phosphorylation of AT1R; and (4) PD98059 blocked Ang II-induced nuclear translocation of AT1Rs. In summary, these observations demonstrate that Ang II-induced phosphorylation of AT1R is mediated by its activation of MAP kinase. A possible role of AT1R translocation into the nucleus on persistent neuromodulatory actions of Ang II has been discussed.
Fine‐scale influences on thaw depth in a forested peat plateau landscape in the Northwest Territories, Canada: Vegetation trumps microtopography

The influence of vegetation and microtopography on fine‐scale variability of thaw depth is largely unknown but potentially important for improving modeling of ecosystem–permafrost interactions. To elucidate their influence, we measured tree density, shrub cover and cryptogam presence (lichen and bryophyte) on forested permafrost peat plateaus in the discontinuous permafrost zone in the southern Northwest Territories, Canada. Greater tree density was associated with shallower thaw depth (approximately one quarter of the variance), whereas shrub cover had a negligible influence on thaw depth. Cryptogam species influenced thaw depth, with greater thaw depth associated with Sphagnum than with Cladonia (a difference on the order of 10%). Greater thaw depth occurred beneath hummocks than beneath hollows (a difference also on the order of 10%). Together, canopy cover, cryptogam species and microforms contribute to a variation of roughly half the variance in thaw depth in the peat plateau landscape.
Spectrum Aggregation: Overview and Challenges

Spectrum aggregation has recently received much attention due to the quick increasing services. This technique makes it possible that multiple spectrum bands are ultilized by the same user to satisfy the large bandwidth demand of the service and achieve better performance. This paper provides an overview on spectrum aggregation. The important research progresses on spectrum aggregation for LTE-Advanced and dynamic spectrum access are briefly described respectively. Finally, some research challenges of protocols and algorithms are addressed for future studies.
Rapid-fire image previews for information navigation

In this paper we consider the role of rapid-fire presentation of images in the service of navigation in information spaces. We presume a model of information navigation in which the user performs a cycle of (pre)viewing, selecting, and moving. Our hypothesis is that images presented to the user in rapid succession can significantly enhance the previewing step, thus optimizing the selection step and improving navigability. We discuss two prototypes for navigation tools in Web information spaces in which images are used as the primary means for presenting meta-information about "upcoming" Web pages. The presentation is modeled as a flow of information streaming to the user, and orientation is visualized through positions in ordered sequences.
Role of amygdala kisspeptin in pubertal timing in female rats

To investigate the mechanism by which maternal obesity disrupts reproductive function in offspring, we examined Kiss1 expression in the hypothalamic arcuate (ARC) and anteroventral periventricular (AVPV) nuclei, and posterodorsal medial amygdala (MePD) of pre-pubertal and young adult offspring. Sprague-Dawley rats were fed either a standard or energy-dense diet for six weeks prior to mating and throughout pregnancy and lactation. Male and female offspring were weaned onto normal diet on postnatal day (pnd) 21. Brains were collected on pnd 30 or 100 for qRT-PCR to determine Kiss1 mRNA levels. Maternal obesity increased Kiss1 mRNA expression in the MePD of pre-pubertal male and female offspring, whereas Kiss1 expression was not affected in the ARC or AVPV at this age. Maternal obesity reduced Kiss1 expression in all three brain regions of 3 month old female offspring, but only in MePD of males. The role of MePD kisspeptin on puberty, estrous cyclicity and preovulatory LH surges was assessed directly in a separate group of post-weanling and young adult female rats exposed to a normal diet throughout their life course. Bilateral intra-MePD cannulae connected to osmotic mini-pumps for delivery of kisspeptin receptor antagonist (Peptide 234 for 14 days) were chronically implanted on pnd 21 or 100. Antagonism of MePD kisspeptin delayed puberty onset, disrupted estrous cyclicity and reduced the incidence of LH surges. These data show that the MePD plays a key role in pubertal timing and ovulation and that maternal obesity may act via amygdala kisspeptin signaling to influence reproductive function in the offspring.