Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining the Order in Which Nmd3p and Rpl10p Load onto Nascent 60S Ribosomal Subunits

ABSTRACT The large ribosomal subunit protein Rpl10p is required for subunit joining and 60S export in yeast. We have recently shown that Rpl10p as well as the cytoplasmic GTPase Lsg1p are required for releasing the 60S nuclear export adapter Nmd3p from subunits in the cytoplasm. Here, we more directly address the order of Nmd3p and Rpl10p recruitment to the subunit. We show that Nmd3p can bind subunits in the absence of Rpl10p. In addition, we examined the basis of the previously reported dominant negative growth phenotype caused by overexpression of C-terminally truncated Rpl10p and found that these Rpl10p fragments are not incorporated into subunits in the nucleus but instead sequester the WD-repeat protein Sqt1p. Sqt1p is an Rpl10p binding protein that is proposed to facilitate loading of Rpl10p into the 60S subunit. Although Sqt1p normally only transiently binds 60S subunits, the levels of Sqt1p that can be coimmunoprecipitated by the 60S-associated GTPase Lsg1p are significantly increased by a dominant mutation in the Walker A motif of Lsg1p. This mutant Lsg1 protein also leads to increased levels of Sqt1p in complexes that are coimmunoprecipitated with Nmd3p. Furthermore, the dominant LSG1 mutant also traps a mutant Rpl10 protein that does not normally bind stably to the subunit. These results support the idea that Sqt1p loads Rpl10p onto the Nmd3p-bound subunit after export to the cytoplasm and that Rpl10p loading involves the GTPase Lsg1p.
MicroRNAs as regulators and mediators of forkhead box transcription factors function in human cancers

Evidence has shown that microRNAs are widely implicated as indispensable components of tumor suppressive and oncogenic pathways in human cancers. Thus, identification of microRNA targets and their relevant pathways will contribute to the development of microRNA-based therapeutics. The forkhead box transcription factors regulate numerous processes including cell cycle progression, metabolism, metastasis and angiogenesis, thereby facilitating tumor initiation and progression. A complex network of protein and non-coding RNAs mediates the expression and activity of forkhead box transcription factors. In this review, we summarize the current knowledge and concepts concerning the involvement of microRNAs and forkhead box transcription factors and describe the roles of microRNAs-forkhead box axis in various disease states including tumor initiation and progression. Additionally, we describe some of the technical challenges in the use of the microRNA-forkhead box signaling pathway in cancer treatment.
Micro/nano-robotics in biomedical applications and its progresses

This article aims at investigating into the backgrounds, applications and the research progresses of micro/nano-robotics in biomedical applications both at home and abroad. Based on the above, the core technology is further summarized into fabrication, control, smart material, simulation, mechanism and biological medicine, etc. The urgently need to be solved, the challenges and the potential trends of micro/nano-robotics in biomedical applications are discussed.
Synthesis of Porous Ni–Co–Mn Oxide Nanoneedles and the Temperature Dependence of Their Pseudocapacitive Behavior

Porous Ni-Co-Mn oxide nanoneedles have been synthesized on Ni foam by a facile one-step hydrothermal method for use as supercapacitor electrodes. Structural and compositional characterizations indicate that Ni, Co and Mn elements are homogeneously distributed within the multi-component metal oxides. Such multi-component metal oxides with a homogenous structure exhibit high specific capacitance of 2023 F g-1 at 1 mA cm-2, high coulombic efficiencies (greater than 99%), and good long-term cycle life (approximately 7% loss in specific capacitance over 3000 charge/discharge cycles) at room temperature. Moreover, the influence of temperature on the electrochemical performance of the electrodes has been characterized at temperatures ranging from 4 to 80°C in aqueous electrolytes. The thermal behavior of the electrodes reveals that elevated operating temperature promotes higher capacitance and lower internal resistance by decreasing the ionic conductivity of the electrolyte and increasing redox reaction rates at the interface of the electrodes and electrolytes. The capacitance of the electrodes increases by 84% at a nominal temerature of 80°C and decreases by 18% at 4°C, compared to that at room temperature (RT). The overall set of results demonstrates that the new Ni-Co-Mn oxide nanoneedle electrodes are promising for high-performance pseudocapacitive electrodes with a wide usable temperature range.
A Model-Free Cross-Coupled Control for Position Synchronization of Multi-Axis Motions: Theory and Experiments

In this brief, a model-free cross-coupled controller is proposed for position synchronization of multi-axis motions. The position synchronization error of each axis is defined as the differential position error between this axis and its two adjacent axes, which is then coupled with the position error to form a coupled position error. A proportional and derivative (PD)-type synchronization controller with feedback of this coupled position error is proposed and proven to guarantee asymptotic convergence to zero of both position and synchronization errors in a setpoint position control. A setpoint tracking controller is further developed by adding feedforward control terms and a saturation function to the PD synchronization controller. The proposed method is easy to implement in practice since it is model free and the control gains are time-invariant. Experiments are performed to verify effectiveness of the proposed approach
A concept-based model for enhancing text categorization

Most of text categorization techniques are based on word and/or phrase analysis of the text. Statistical analysis of a term frequency captures the importance of the term within a document only. However, two terms can have the same frequency in their documents, but one term contributes moreto the meaning of its sentences than the other term. Thus, the underlying model should indicate terms that capture these mantics of text. In this case, the model can capture terms that present the concepts of the sentence, which leads todiscover the topic of the document. A new concept-based model that analyzes terms on the sentence and document levels rather than the traditional analysis of document only is introduced. The concept-based model can effectively discriminate between non-important terms with respect to sentence semantics and terms which hold the concepts that represent the sentence meaning. The proposed model consists of concept-based statistical analyzer, conceptual ontological graph representation,and concept extractor. The term which contributes to the sentence semantics is assigned two different weights by the concept-based statistical analyzer and the conceptual ontological graph representation. These two weights are combined into a new weight. The concepts that have maximum combined weights are selected by the concept extractor. A set of experiments using the proposed concept-basedmodel on different datasets in text categorization is conducted. The experiments demonstrate the comparison between traditional weighting and the concept-based weighting obtained by the combined approach of the concept-based statistical analyzer and the conceptual ontological graph. The evaluation of results is relied on two quality measures, the Macro-averaged F1 and the Error rate. These quality measures are improved when the newly developedconcept-based model is used to enhance the quality of thetext categorization.
Competition, Transmission and Bank Pricing Policies: Evidence from Belgian Loan and Deposit Markets

This paper analyses the pass-through of money market rates to retail interest rates in the Belgian banking market using disaggregate data and allowing for heterogeneous price setting behavior. We find that 1) corporate loans are priced more competitively than consumer loans, 2) pass-through is higher for products with longer maturities, 3) EMU did not increase price competition, 4) bank behavior is consistent with the presence of menu costs, and 5) existing empirical evidence may underestimate adjustment speed. Furthermore, heterogeneous price setting among banks is driven by market power as well as the bank lending channel.
Estimation of DOA and phase error using a partly calibrated sensor array with arbitrary geometry

A new method is presented to effectively estimate the direction-of-arrival (DOA) of a source signal and the phase errors of a sensor array with arbitrary geometry. Assuming that one sensor (except the reference one) has been calibrated, the proposed method appropriately reconstruct the data matrix and establish a series of linear equations with respect to the unknown parameters through eigenvalue decomposition (EVD). We build a LS problem with a quadratic constraint and solve it by two approaches. Unlike the conventional methods which are limited to specific array geometries, the proposed can be applied to arbitrary arrays. Moreover, it only requires one calibrated sensor, which may not be consecutively spaced to the reference one. The effectiveness of the proposed method is validated by simulation results.
Based on Isolated Saliency or Causal Integration? Toward a Better Understanding of Human Annotation Process using Multiple Instance Learning and Sequential Probability Ratio Test

Human perception is capable of integrating local events to generate an overall impression at the global level; this is evident in daily life and is utilized repeatedly in behavioral science studies to bring objective measures into studies of human behavior. In this work, we explore two hypotheses considering whether it is the isolated-saliency or the causal-integration of information that can trigger the global perceptual behavioral ratings as trained annotators engage in tasks of observational coding. We carry out analyses using Multiple Instance Learning and Sequential Probability Ratio Test in a corpus of real and spontaneous distressed couples’ interaction with global sessionlevel abstract behavioral coding done by trained human annotators. We present various analyses based on different behavioral detection schemes demonstrating the potential of utilizing these algorithms in bringing insights into the human annotation process. We further show that while annotating behaviors with more positive impression, annotators gather information throughout the session compared to behaviors with more negative impression, where a single salient instance is enough to trigger the final global decision.
“Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants

Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater by wasting the biomass. However, glycogen accumulating organisms (GAOs) may reduce the EBPR efficiency as they compete for substrates with PAOs, but do not store excessive amounts of polyphosphate. PAOs and GAOs are thought to be phylogenetically unrelated, with the model PAO being the betaproteobacterial “Candidatus Accumulibacter phosphatis” (Accumulibacter) and the model GAO being the gammaproteobacterial “Candidatus Competibacter phosphatis”. Here, we report the discovery of a GAO from the genus Propionivibrio, which is closely related to Accumulibacter. Propionivibrio sp. are targeted by the canonical fluorescence in situ hybridization probes used to target Accumulibacter (PAOmix), but do not store excessive amounts of polyphosphate in situ. A laboratory scale reactor, operated to enrich for PAOs, surprisingly contained co-dominant populations of Propionivibrio and Accumulibacter. Metagenomic sequencing of multiple time-points enabled recovery of near complete population genomes from both genera. Annotation of the Propionivibrio genome confirmed their potential for the GAO phenotype and a basic metabolic model is proposed for their metabolism in the EBPR environment. Using newly designed fluorescence in situ hybridization (FISH) probes, analyses of full-scale EBPR plants revealed that Propionivibrio is a common member of the community, constituting up to 3% of the biovolume. To avoid overestimation of Accumulibacter abundance in situ, we recommend the use of the FISH probe PAO651 instead of the commonly applied PAOmix probe set.
Stochastic dynamics of remote knock-on permeation in biological ion channels

Brownian dynamics simulations provide evidence for a remote knock-on mechanism facilitating the permeation of a biological ion channel by an ion that is initially trapped at the selectivity filter (SF). Unlike the case of conventional direct knock-on, the second ion that instigates permeation does not need to enter the channel. Nor does it necessarily take the place of the permeating ion at the SF, and it can even be of a different ionic species. The study is based on the simultaneous, self-consistent, solution of the coupled Poisson and Langevin equations for a simple generic model, taking account of all the charges present. The new permeation mechanism involves electrostatic amplification attributable to the permittivity mismatch between water and protein: the arrival of the instigating ion at the channel entrance reduces the exit barrier for the ion trapped at the SF, facilitating escape.
Efficient Incremental Dependency Parsing

This paper describes an eﬃcient method of incremental dependency parsing based on phrase structure grammar with the dependency relation. The reachability relation between syntactic categories is utilized for connecting a head word with a dependent word simultaneously with the inputs. The method does not need to construct the whole parse tree of an initial fragment on the word-by-word basis, and thus can be expected to be usable for simultaneous spoken language processing. An experiment on the ATIS corpus has shown the technique of utilizing the reachability to be eﬀective for reducing processing time of the incremental dependency parsing.
Dynamics of functional connectivity in visual cortical networks : An overview

The aim of the Royaumont Symposium was to review various dynamic aspects of adaptive changes in functional connectivity, expressed in cortical networks during development, learning. and possibly during recognition and cognitive processing. The link between the various experimental and theoretical models was the comparison of cellular and molecular mechanisms that could be involved in the upand down-regulation of functional connectivity, over different time scales. These processes have been investigated using several approaches in parallel: 1) at the molecular/subcellular level. to identify postsynaptic receptors WMDA, mGluR) and second messengers (calcium. protein kinases and phosphatases) involved in the induction of synaptic potentiation and depression. and to characterize diffusible factors (NO), released preor postsynaptically. involved in the spatial generalization of local changes to neighboring synapses; 2) at the level of integrating networks. to develop electrophysiological (single and multiple recording), pharmacological and optical imaging techniques in order to compare the dynamics of adaptive processes put into play during the natural development of cortical specificity and connectivity, r~rsus those triggered during forced regimes of temporal correlations between preand post synaptic activities. Both in vitro and in rive approaches have been combined in the primary visual cortex of the developing and adult vertebrate (rat, guinea-pig. ferret, cat and monkey). The various forms of ‘slow’ synaptic plasticity. demonstrated during epigenesis and selective phases of learning in the adult, can be compared with ‘fast’ forms of functional coupling (or synchronous firing) shown to develop during the time span required for perception and cognitive processing. Phenomenology of the dynamics in functional connectivity and their relative dependence on temporal correlation in neuronal activity have been analyzed in each of these situations. Experimental results have been compared at different levels of neuronal integration (synapse, column, map and cell assembly) in order to gain a better understanding of functional grouping within cortical networks.
Phrase Generalization: a Corpus Study in Multi-Document Abstracts and Original News Alignments

Content can be expressed at different levels of speciﬁcity, varying the amount of detail presented to the reader. The need to transform speciﬁc content into more general form naturally arises in summarization, where people and machines need to convey the gist of a text within imposed space constraints. Completely removing sentences and phrases is one way to reduce the level of detail. The bulk of work on summarization content selection and compression deal with these tasks. In this paper, we present a corpus study on a more subtle and under-studied phenomenon: noun phrase generalization. Based on multi-document news and abstract alignments at the phrase level, we arrive at a ﬁve category classiﬁcation scheme and ﬁnd that the most common category requires semantic interpretation and inference. The others rely on lexical substitution or deletion of details from the original expression. We provide a systematic analysis, elucidating the capabilities needed for automating the generation of more general or more speciﬁc references.
Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) of Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general

ABSTRACT The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively during Quaternary glacio-eustatic land connections, whereas the Bornean and Palawan populations did not. Unlike the other Greater Sunda Islands, Palawan has not been attached by a land bridge to the rest of Sundaland for at least one million years, and its relative isolation has prevented extensive intermixing between Palawan's and other Sunda populations. Thus, the Palawan population appears to be on its own evolutionary trajectory. The ability to demonstrate extensive interbreeding among some Sunda island populations, but not others, illustrates the practicality of testing Gill's (2014) “null hypothesis” that morphologically distinct populations on different islands are different species unless a compelling argument can be made to the contrary. In this case, Rufous-tailed Tailorbird morphology provided little or misleading evidence of the extent of interbreeding, whereas modern genetic analysis provided a clear view.
Green Synthesis of a Functionalized Zirconium-Based Metal–Organic Framework for Water and Ethanol Adsorption

Aqueous synthesis of metal–organic frameworks (MOFs) at room temperature offers many advantages such as reduction in the generation of toxic byproducts and operation costs, as well as increased safety in the material’s production. Functional group-bearing MOFs have received growing attention compared to nonfunctionalized analogues due to enhanced adsorption properties of the former in many cases. Here, we report an aqueous solution-based synthesis of a robust zirconium MOF, UiO-66-NO2, at room temperature. We evaluated the phase purity, porosity, thermal stability, particle morphology and size of the resulting material. High uptake, as well as near complete recyclability of water and ethanol vapor isotherms at room temperature supports the potential of UiO-66-NO2 as a solid adsorbent in adsorption-based cooling applications or water harvesting systems.
Antimicrobial susceptibility testing for Helicobacter pylori isolates from Brazilian children and adolescents: Comparing agar dilution, E-test, and disk diffusion

Antimicrobial susceptibility testing for Helicobacter pylori is increasingly important due to resistance to the most used antimicrobials agents. Only agar dilution method is approved by CLSI, but it is difficult to perform routinely. We evaluated the reliability of E-test and disk diffusion comparing to agar dilution method on Helicobacter pylori antimicrobial susceptibility testing. Susceptibility testing was performed for amoxicillin, clarithromycin, furazolidone, metronidazole and tetracycline using E-test, disk-diffusion and agar dilution method in 77 consecutive Helicobacter pylori strains from dyspeptic children and adolescents. Resistance rates were: amoxicillin - 10.4%, 9% and 68.8%; clarithromycin - 19.5%, 20.8%, 36.3%; metronidazole - 40.2%33.7%, 38.9%, respectively by agar dilution, E-test and disk diffusion method. Furazolidone and tetracycline showed no resistance rates. Metronidazole presented strong correlation to E-test (r = 0.7992, p < 0.0001) and disk diffusion method (r=-0.6962, p < 0.0001). Clarithromycin presented moderate correlation to E-test (r = 0.6369, p < 0.0001) and disk diffusion method (r=−0.5656, p < 0.0001). Amoxicillin presented weak correlation to E-test (r = 0.3565, p = 0.0015) and disk diffusion (r=−0.3565, p = 0.0015). Tetracycline presented weak correlation with E-test (r = 0.2346, p = 0.04) and furazolidone to disk diffusion (r=−0.0288, p = 0.8038). E-test presented better agreement with gold standard. It is an easy and reliable method for Helicobacter pylori susceptibility testing. Disk diffusion method presented high disagreement and high rates of major errors.
Comparison of Software Life Cycle Models

Computer software continues to be the single most important technology on the world stage. Software Engineering is the establishment and use of sound engineering principles in order to obtain economically software that is reliable and work efficiently on real machines. Software development organizations follow some process when developing a software product. A variety of life cycle models has been proposed and is based on tasks involved in developing and maintaining software. This paper presents a comparison between various software life cycle models used for software development along with their advantages and disadvantages.