Miracle-dz/UniFAR-FTUs huggingface dataset:
Yng1p Modulates the Activity of Sas3p as a Component of the Yeast NuA3 Histone Acetyltransferase Complex

ABSTRACT The mammalian ING1 gene encodes a tumor suppressor required for the function of p53. In this study we report a novel function for YNG1, a yeast homolog of ING1. Yng1p is a stable component of the NuA3 histone acetyltransferase complex, which contains Sas3p, the yeast homolog of the mammalian MOZ proto-oncogene product, as its catalytic subunit. Yng1p is required for NuA3 function in vivo but surprisingly is not required for the integrity of the complex. Instead, we find that Yng1p mediates the interaction of Sas3p with nucleosomes and is thus required for the ability of NuA3 to modify histone tails. These data, and the observations that other ING1 homologs are found in additional yeast complexes that posttranslationally modify histones, suggest that members of the ING1 class of proteins may have broad roles in enhancing or modifying the activities of chromatin-modifying complexes, thereby regulating their activities in transcription control.
Investigating CNS synaptogenesis at single-synapse resolution by combining reverse genetics with correlative light and electron microscopy

Determining direct synaptic connections of specific neurons in the central nervous system (CNS) is a major technical challenge in neuroscience. As a corollary, molecular pathways controlling developmental synaptogenesis in vivo remain difficult to address. Here, we present genetic tools for efficient and versatile labeling of organelles, cytoskeletal components and proteins at single-neuron and single-synapse resolution in Drosophila mechanosensory (ms) neurons. We extended the imaging analysis to the ultrastructural level by developing a protocol for correlative light and 3D electron microscopy (3D CLEM). We show that in ms neurons, synaptic puncta revealed by genetically encoded markers serve as a reliable indicator of individual active zones. Block-face scanning electron microscopy analysis of ms axons revealed T-bar-shaped dense bodies and other characteristic ultrastructural features of CNS synapses. For a mechanistic analysis, we directly combined the single-neuron labeling approach with cell-specific gene disruption techniques. In proof-of-principle experiments we found evidence for a highly similar requirement for the scaffolding molecule Liprin-α and its interactors Lar and DSyd-1 (RhoGAP100F) in synaptic vesicle recruitment. This suggests that these important synapse regulators might serve a shared role at presynaptic sites within the CNS. In principle, our CLEM approach is broadly applicable to the developmental and ultrastructural analysis of any cell type that can be targeted with genetically encoded markers. Summary: Genetic tools, and 3D correlative light and electron microscopy allow the dissection of the mechanisms governing synaptogenesis at single-cell resolution in the Drosophila CNS.
Evaluation of the cytotoxicity of cigarette smoke total particulate matter using three in vitro assays and two types of cells

Abstract In vitro cytotoxicity assays can be used to evaluate potential toxicological effects of tobacco products. Total particulate matter (TPM) from mainstream cigarette smoke trapped by a Cambridge filter is used widely for biological evaluation of smoke. This study compared neutral red uptake (NRU), lactate dehydrogenase (LDH) activity and WST-1 assays for assessing the cytotoxicity of TPM, and evaluated the sensitivity of Chinese hamster ovary (CHO) cells and human lung adenocarcinoma epithelial cell line (A549 cells) to TPM-induced cytotoxic effects. The results indicate that NRU and WST-1 assays are preferable to LDH activity assay for assessing the TPM-induced cytotoxicity, and NRU assay might be more sensitive than WST-1 assay. The cytotoxicity of 3R4F reference cigarettes and two commercial brands of cigarettes were tested by NRU assay in CHO and A549 cells. The results showed that EC50 values in CHO cells treated with TPM were lower than EC50 values in A549 cells, indicating CHO cells are more sensitive to TPM-induced cytotoxic effects than A549 cells.
Eliminating Exception Handling Errors with Dependability Cases: A Comparative, Empirical Study

Programs fail mainly for two reasons: logic errors in the code and exception failures. Exception failures can account for up to two-thirds of system crashes, hence, are worthy of serious attention. Traditional approaches to reducing exception failures, such as code reviews, walkthroughs, and formal testing, while very useful, are limited in their ability to address a core problem: the programmer's inadequate coverage of exceptional conditions. The problem of coverage might be rooted in cognitive factors that impede the mental generation (or recollection) of exception cases that would pertain in a particular situation, resulting in insufficient software robustness. This paper describes controlled experiments for testing the hypothesis that robustness for exception failures can be improved through the use of various coverage-enhancing techniques: N-version programming, group collaboration, and dependability cases. N-version programming and collaboration are well known. Dependability cases, derived from safety cases, comprise a new methodology based on structured taxonomies and memory aids for helping software designers think about and improve exception handling coverage. All three methods showed improvements over control conditions in increasing robustness to exception failures but dependability cases proved most efficacious in terms of balancing cost and effectiveness.
Nitrogen/fluorine-codoped rutile titania as a stable oxygen-evolution photocatalyst for solar-driven Z-scheme water splitting

Nitrogen/fluorine-codoped rutile TiO2 (R-TiO2:N,F) was newly synthesized, and its photocatalytic activity for water oxidation was evaluated. R-TiO2:N,F could be prepared by nitridation of the rutile TiO2 (R-TiO2) and (NH4)2TiF6 mixture at 773 K. The prepared samples produced O2 from aqueous AgNO3 solution under visible light irradiation, while R-TiO2 nitrided at the same temperature without any fluorine source showed negligible activity. The highest activity was obtained with the sample prepared at the (NH4)2TiF6/R-TiO2 ratio of 15/85, exhibiting water oxidation activity even in the presence of a reversible electron acceptor such as IO3− or Fe3+ with the aid of a RuO2 cocatalyst. Stoichiometric water splitting into H2 and O2 was achieved using a mixture of Ru/SrTiO3:Rh and RuO2/TiO2:N,F in the presence of [Co(bpy)3]3+/2+ (bpy = 2,2′-bipyridine) as a shuttle redox mediator without noticeable degradation of activity under visible light and even under AM1.5G simulated sunlight. Transient absorption spectroscopy revealed that appropriate nitrogen/fluorine codoping reduces the density of mid-gap states working as deep traps of photogenerated electrons, and increases the number of free electrons compared to only nitrogen-doped R-TiO2. Experimental results highlighted that the photocatalytic activity of R-TiO2:N,F could be enhanced by improving visible-light absorption capability through N/F codoping while suppressing the density of deep trap sites.
Augmenting a portal with conceptual metadata for improved user search and browsing

There has been a long relationship between the fields of information management and natural language processing, going back at least as far as [9], and revived in many of the text retrieval subtasks pursued under the aegis of the annual TREC conferences[4]. It has been assumed that linguistic processing can only improve performance in the processes of indexing and retrieval in full-text information services, which is one way to describe the Refugee Studies Web. Linguistic processing either analyzes or generates text (or spoken utterances which are not discussed here). Many different types of analysis are possible, and may be classified on several different axes.
Epidemiology of chronic venous disease

Abstract Chronic venous disease of the legs occurs commonly in the general population in the Western world. Estimates of the prevalence of varicose veins vary widely from 2–56% in men and from 1–60% in women. These variations reflect differences in variability of study populations including age, race and gender, methods of measurement and disease definition. Definitions of chronic venous disease may rely on reports of varicose veins by study participants, based on self-diagnosis or recall of a diagnosis, or on a standardized physical examination. Venous ulceration is less common, affecting approximately 0.3% of the adult population. Age and pregnancy have been established as risk factors for developing varicose veins. Evidence on other risk factors for venous disease is inconclusive. Prolonged standing has been proposed, but results of studies should be interpreted with caution given the difficulty in measuring levels of posture. Obesity has been suggested as a risk factor in women, but appears to be an aggravating factor rather than a primary cause. Other postulated risk factors include dietary intake and smoking, but evidence is lacking. Longitudinal studies using standardized methods of evaluation are required before the true incidence of chronic venous disease and associated risk factors can be determined.
Coupling and cohesion as modularization drivers: are we being over-persuaded?

For around three decades software engineering gurus have "sold" us the ideal of minimal coupling and maximal cohesion at all levels of abstraction as a way to reduce the effort to understand and maintain software systems. The object oriented paradigm brought a new design philosophy and encapsulation mechanisms that apparently would help us to achieve that desideratum. However, after a decade where this paradigm has emerged as the dominant one, we are faced with practitioners' reality: coupling and cohesion do not seem to be the dominant driving forces when it comes to modularization. This conclusion was based on a relatively large sample of heterogeneous systems. We describe an environment that allows us not only to assess this reality but also to derive better modularization solutions in what concerns coupling and cohesion. These solutions are generated by means of cluster analysis techniques and partially preserve the original modularization criteria. We believe this approach can be of great help in reengineering actions of object oriented legacy systems.
Service excellence in health care.

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The Stochastic Edge in Adaptive Evolution

In a recent article, Desai and Fisher proposed that the speed of adaptation in an asexual population is determined by the dynamics of the stochastic edge of the population, that is, by the emergence and subsequent establishment of rare mutants that exceed the fitness of all sequences currently present in the population. Desai and Fisher perform an elaborate stochastic calculation of the mean time τ until a new class of mutants has been established and interpret 1/τ as the speed of adaptation. As they note, however, their calculations are valid only for moderate speeds. This limitation arises from their method to determine τ: Desai and Fisher back extrapolate the value of τ from the best-fit class's exponential growth at infinite time. This approach is not valid when the population adapts rapidly, because in this case the best-fit class grows nonexponentially during the relevant time interval. Here, we substantially extend Desai and Fisher's analysis of the stochastic edge. We show that we can apply Desai and Fisher's method to high speeds by either exponentially back extrapolating from finite time or using a nonexponential back extrapolation. Our results are compatible with predictions made using a different analytical approach (Rouzine et al.) and agree well with numerical simulations.
Particle manipulation in a microfluidic channel with an electronically controlled linear piezoelectric array

Ultrasonic standing wave manipulation has been proved to be a simple, robust technology to be integrated in microfluidic systems for a range of applications such as particle filtration and concentration, particle trapping and washing, and sensor enhancement. Here we report recent progress in the design, fabrication and experimental demonstration of an electronically controlled ultrasonic array device used for 1-D manipulation of particles along a microfluidic channel. In a previous paper [1], the particle manipulation feasibility has been demonstrated by a 12 element, 500 μm pitch array device. In this paper, an improved 30-element, 200 μm pitch array device made from PZ26 piezoelectric composite has been fabricated and connected to control electronics. The control system comprises a Xilinx Spartan 3a FPGA development board and bespoke analogue driving circuitry, designed for signal multiplexing for array element excitation. A rectangular capillary forming a half wavelength resonance microfluidic chamber was coupled to the array to make a multilayer planar resonator. Manipulation under electronic control was demonstrated with 10 μm fluorescent microspheres suspended in water.
Interactive Music Summarization based on GTTM

This paper presents a music summarization system called “Papipuun” that we are developing. Papipuun performs quick listening in a manner similar to a stylus skipping on a scratched record, but the skipping occurs correctly at punctuations of musical phrases, not arbitrarily. First, we developed a method for representing polyphony based on time-span reduction in the generative theory of tonal music (GTTM) and the deductive object-oriented database (DOOD). The operation, least upper bound, plays an important role in similarity checking of polyphonies represented in our method. Next, in a preprocessing phase, a user analyzes a set piece by the time-span reduction, using a dedicated tool called TS-Editor. For the real-time phase, the user interacts with the main system, Summarizer, to perform music summarization. Summarizer discovers a piece structure by means of similarity checking. When the user identifies the fragments to be skipped, Summarizer deletes them and concatenates the rest. Papipuun can produce a music summarization of good quality, reflecting the atmosphere of an entire piece through interaction with the user.
Voting base online sequential extreme learning machine for multi-class classification

In this paper, we propose a voting based online sequential extreme learning machine (VOS-ELM) for single hidden layer feedforward networks (SLFNs) to perform the online sequential multi-class classification. Utilizing the recent voting based extreme learning machine (V-ELM) and the online sequential extreme learning machine (OS-ELM), the newly developed VOS-ELM is able to classify online sequences by learning data one-by-one or chunk-by-chunk with fixed or varying chunk size and to reach a higher classification accuracy than the original OS-ELM. Simulations on several real world classification datasets show that VOS-ELM outperforms OS-ELM as well as several state-of-the-art online sequential algorithms.
Capturing the mutational landscape of the beta-lactamase TEM-1

Adaptation proceeds through the selection of mutations. The distribution of mutant fitness effect and the forces shaping this distribution are therefore keys to predict the evolutionary fate of organisms and their constituents such as enzymes. Here, by producing and sequencing a comprehensive collection of 10,000 mutants, we explore the mutational landscape of one enzyme involved in the spread of antibiotic resistance, the beta-lactamase TEM-1. We measured mutation impact on the enzyme activity through the estimation of amoxicillin minimum inhibitory concentration on a subset of 990 mutants carrying a unique missense mutation, representing 64% of possible amino acid changes in that protein reachable by point mutation. We established that mutation type, solvent accessibility of residues, and the predicted effect of mutations on protein stability primarily determined alone or in combination changes in minimum inhibitory concentration of mutants. Moreover, we were able to capture the drastic modification of the mutational landscape induced by a single stabilizing point mutation (M182T) by a simple model of protein stability. This work thereby provides an integrated framework to study mutation effects and a tool to understand/define better the epistatic interactions.
A Selective Encryption for Heterogenous Color JPEG Images Based on VLC and AES Stream Cipher

Nowadays, the most important engine to provide confidentiality is encryption. Therefore, the classical and modern ciphers are not suitable for huge quantity of data in real-time environment. Selective encryption (SE) is an approach to encode only the most important portion of the data in order to provide a proportional privacy and to reduce computational requirements. The objective of our work is to leave free the low-resolution image and give full-resolution access only for authorized person. This approach is based on AES stream ciphering using VLC (Variable Length Coding) of the Huffman's vector. The proposed scheme allows decryption of a specific region of image and result in a significant reduction in encrypting and decrypting processing time. It also provides a constant bit rate and keep the JPEG bit-stream compliance. We have illustrated our method on a digital painting of the Louvre Museum of Paris, France.
Surfactant Collectins and Innate Immunity

Respiratory pathogens encounter various lines of defenses before infection of the host is established. The innate immune response represents an important first-line protection mechanism against potentially pathogenic microorganisms during early stages of infection of the naive host. Important players in this host defense system are ‘collectins’, a class of soluble innate immune proteins. Well-characterized members of the collectin family are the surfactant proteins A (SP-A) and D (SP-D). These collectins are expressed in the lung and also in extrapulmonary mucosal tissues. Collectins are secreted as multimers resulting in trimeric clustering of the lectin domains which enables recognition of evolutionary conserved sugar patterns present on the surface of a large variety of pathogens. Binding to collectins may lead to direct agglutination and neutralization of pathogens, to opsonization in order to present bound microbes directly to phagocytes, to modulation of the inflammatory response and to regulation of dendritic cell and T cell functions. In pulmonary tissue, this early acute-phase-like response can be regarded as a crucial layer of protection against a vast array of pathogens that escape the physical barriers and threaten to infect the delicate respiratory epithelium. An important clinical application may be the inhalation, or instillation of collectin-based drugs as part of surfactant therapy, to prevent and treat infectious and inflammatory diseases of newborn infants.
Dietary n‐3 long‐chain polyunsaturated fatty acids modify phosphoenolpyruvate carboxykinase activity and lipid synthesis from glucose in adipose tissue of rats fed a high‐sucrose diet

Long‐chain polyunsaturated n‐3 fatty acids (n‐3 LCPUFAs) have hypolipidemic effects and modulate intermediary metabolism to prevent or reverse insulin resistance in a way that is not completely elucidated. Here, effects of these fatty acids on the lipid profile, phosphoenolpyruvate carboxykinase (PEPCK) activity, lipid synthesis from glucose in epididymal adipose tissue (Ep‐AT) and liver were investigated. Male rats were fed a high‐sucrose diet (SU diet), containing either sunflower oil or a mixture of sunflower and fish oil (SU–FO diet), and the control group was fed a standard diet. After 13 weeks, liver, adipose tissue and blood were harvested and analysed. The dietary n‐3 LCPUFAs prevented sucrose‐induced increase in adiposity and serum free fat acids, serum and hepatic triacylglycerol and insulin levels. Furthermore, these n‐3 LCPUFAs decreased lipid synthesis from glucose and increased PEPCK activity in the Ep‐AT of rats fed the SU–FO diet compared to those fed the SU diet, besides reducing lipid synthesis from glucose in hepatic tissue. Thus, the inclusion of n‐3 LCPUFAs in the diet may be beneficial for the prevention or attenuation of dyslipidemia and insulin resistance, and for reducing the risk of related chronic diseases. Copyright © 2013 John Wiley & Sons, Ltd.
Effect of heat treatment on corrosion behavior of duplex stainless steel in orthodontic applications

Heat treatment is necessary for duplex stainless steel (DSS) to remove or dissolve intermetallic phases, to remove segregation and to relieve any residual thermal stress in DSS, which may be formed during production processes. In the present study, the corrosion resistance of a DSS in artificial saliva was studied by potentiodynamic measurements. The microstructure was investigated by scanning electron microscopy (SEM),x-ray diffraction (XRD) and Vickers hardness (HV). The properties were tested in as–received and in thermally treated conditions (800–900 °C, 2–8 min). The research aims to evaluate the capability of DSS for orthodontic applications, in order to substitute the austenitic grades. The results indicate that the corrosion resistance is mainly affected by the ferrite/austenite ratio. The best result was obtained with a treatment at 900 °C for 2 min.
Eliciting Requirements for Industrial Design Using the Knowledge Management Strategy for Requirements Engineering

Eliciting sufficient high-quality knowledge from individuals to design a new product or solution is a very time-consuming and expensive activity, especially in domains where the knowledge is informally stated, partially complete, implicitly assumed, tacit and unstructured. The KMoS-RE strategy has the aim of acquiring and structuring the most quantity of knowledge, either tacit or explicit, in order to incorporate it into a specification that cover the needs and expectations of clients and users. The goal of this paper is to present the application of the KMoS-RE strategy in an industrial design real case. The case study showed that the strategy is effective eliciting and structuring knowledge of an informally structured and complex domain, that the artifacts proposed by the strategy act as an effective means of communication among the involved, and that the strategy evolves the knowledge of all involved in any application domain in a short time, which leads to better design decisions.
Factors Predictive for Incidence and Remission of Internet Addiction in Young Adolescents: A Prospective Study

The aim of the study is to determine the incidence and remission rates for Internet addiction and the associated predictive factors in young adolescents over a 1-year follow-up. This was a prospective, population-based investigation. Five hundred seventeen students (267 male and 250 female) were recruited from three junior high schools in southern Taiwan. The factors examined included gender, personality, mental health, self-esteem, family function, life satisfaction, and Internet activities. The result revealed that the 1-year incidence and remission rates for Internet addiction were 7.5% and 49.5% respectively. High exploratory excitability, low reward dependence, low self-esteem, low family function, and online game playing predicted the emergency of the Internet addiction. Further, low hostility and low interpersonal sensitivity predicted remission of Internet addiction. The factors predictive incidence and remission of Internet addiction identified in this study could be provided for prevention and promoting remission of Internet addiction in adolescents.