Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential decay of RNA of the CFA/I fimbrial operon and control of relative gene expression

CFA/I fimbriae on human enterotoxigenic Escherichia coli are composed of the CfaB protein, the product of the second gene of the CFA/I operon. We show here that CfaB is expressed at a higher level than other proteins of the CFA/I operon. mRNA encoding the CfaB protein is much more abundant than mRNA encoding CfaA, the first protein, together with CfaB or mRNA encoding CfaA only. Only one promoter, upstream of cfaA, is present. These data indicate that a primary transcript containing cfaA and cfaB is processed into a cfaA-specific mRNA and a cfaB-specific mRNA. The cfaA mRNA is unstable, while the cfaB mRNA is stable and therefore accumulates in CFA/I-producing E. coli. The cfaB mRNA is probably stabilized by a stem-loop structure downstream of the cfaB gene. No distinct mRNA fragments could be detected encoding the other two proteins, CfaC and CfaE, of the CFA/I operon. These results indicate that cfaC- and cfaE-specific mRNAs degrade very rapidly and/or are produced in small amounts.
Energy-optimal configuration selection for manycore chips with variation

Operating chips at high energy efficiency is one of the major challenges for modern large-scale supercomputers. Low-voltage operation of transistors increases the energy efficiency but leads to frequency and power variation across cores on the same chip. Finding energy-optimal configurations for such chips is a hard problem. In this work, we study how integer linear programming techniques can be used to obtain energy-efficient configurations of chips that have heterogeneous cores. Our proposed methodologies give optimal configurations as compared with competent but sub-optimal heuristics while having negligible timing overhead. The proposed ParSearch method gives up to 13.2% and 7% savings in energy while causing only 2% increase in execution time of two HPC applications: miniMD and Jacobi, respectively. Our results show that integer linear programming can be a very powerful online method to obtain energy-optimal configurations.
Interactive recovery from speech recognition errors in speech user interfaces

The authors present a multimodal approach to interactive recovery from speech recognition errors for the design of speech user interfaces. They propose a framework to compare various error recovery methods, arguing that a rational user will prefer interaction methods which provide an optimal trade off between accuracy, speed and naturalness. They describe a prototypical implementation of multimodal interactive error recovery and present results from a preliminary evaluation in form filling and speech to speech translation tasks.
Comparing brain‐derived neurotrophic factor and ciliary neurotrophic factor secretion of induced neurotrophic factor secreting cells from human adipose and bone marrow‐derived stem cells

Adipose derived stem cells (ADSCs) and bone marrow stem cells (BMSCs) may be equally beneficial in treating neurodegenerative diseases. However, ADSCs have practical advantages. In this study, we aimed to induce neurotrophic factors secreting cells in human ADSCs. Then, we compared the level of brain‐derived neurotrophic factor (BDNF) and ciliary neurotrophic factor (CNTF) secretion in neurotrophic factors secreting cells from human adipose and bone marrow‐derived stem cells. Isolated human ADSCs and BMSCs were induced to neurotrophic factor (NTF)‐secreting cells. The levels of expression and secretion of BDNF and CTNF of induced cells were assessed using immunocytochemical, Real‐Time polymerase chain reaction, and enzyme linked immunosorbent assay (ELISA). The level of BDNF significantly increased in both the induced mesenchymal stem cells (MSCs) relative to ADSCs and the BMSCs (P < 0.01). Moreover, ELISA analysis showed that the release of BDNF in the induced BMSCs was almost twofold more than the induced ADSCs. Overall, NTF‐secreting factor cells derived BMSCs and ADSCs could secret a range of different growth factors. Therefore, the variation in neurotrophic factors of different induced MSC populations suggest the possible beneficial effect of each specific kind of neurotrophic factor secreting cells for the treatment of a particular neurodegenerative disease.
An Identity Authentication Scheme for Opportunistic Network Based on Multidimensional Scaling

This paper proposed an identity authentication scheme for opportunistic networks based on multidimensional scaling. The scheme provides a method to evaluate the trust relationship between nodes by calculating the relationship strength using the social context based on MDS and avoid the security issues caused by invalid certification from malicious nodes. Since there are no complete links between nodes in opportunistic network, M-CCIA establishes a trusted certificate network between nodes which implements the distributed identity authentication. Simulation results show that our security scheme will not induce any negative impact on the average delay, but will achieve higher delivery probability and detectable rate of malicious nodes and also lower routing overhead rate.
The interactive effects of calcium concentration and temperature on the survival and reproduction of Daphnia pulex at high and low food concentrations

We reared Daphnia pulex in a fully defined medium at seven calcium (Ca) concentrations (0.1, 0.5, 1, 1.5, 2, 5, and 10 mg Ca L−1), two mixed algal densities (high food: 30 mg chlorophyll a L−1 and low food: 3 mg Chl a L−1), and four temperatures (20ºC, 24ºC, 28ºC, and 32ºC) in a fully factorial design. The minimum Ca concentration required for the survival and reproduction of D. pulex was between 0.1 and 0.5 mg Ca L−1. Daphniids reared at 0.1 mg Ca L−1 lived no longer than 10 d and did not reproduce. Although offspring were produced at 0.5 mg Ca L−1 and above, reproduction was reduced below 1.5 mg Ca L−1 due to delays in maturity and reductions in both the brood size and number of broods produced within the 15 d of the experiment. As a result, the intrinsic rate of natural increase, r, decreased dramatically between 1.5 and 1 mg Ca L−1, and was undefined at 0.1 mg Ca L−1. Higher temperatures and reduced algal biomass enhanced the susceptibility of D. pulex to low Ca concentrations by raising the reproductive threshold to 1.5 mg Ca L−1. Thermal stress at 32ºC was so great that daphniids lived no longer than 5 d and did not reproduce. Hence, r was undefined at 32ºC. In order to sustain D. pulex populations and potentially other Ca‐sensitive daphniids, fresh waters must maintain a Ca concentration of at least 0.5 mg Ca L−1, although concentrations as high as 1.5 mg Ca L−1 may be required for daphniids to withstand the concurrent reductions in algal biomass and rising water temperatures that are now commonplace on the south‐central Canadian Shield.
A language-independent method for the extraction of RDF verbalization templates

With the rise of the Semantic Web more and more data become available encoded using the Semantic Web standard RDF. RDF is faced towards machines: designed to be easily processable by machines it is difficult to be understood by casual users. Transforming RDF data into human-comprehensible text would facilitate non-experts to assess this information. In this paper we present a languageindependent method for extracting RDF verbalization templates from a parallel corpus of text and data. Our method is based on distant-supervised simultaneous multi-relation learning and frequent maximal subgraph pattern mining. We demonstrate the feasibility of our method on a parallel corpus of Wikipedia articles and DBpedia data for English and German.
Guidelines for Teaching Art to Students from Urban High-Poverty Backgrounds

This study concerns the use of character education practices in schools and how these practices can be integrated into the art education curriculum to benefit students from urban highpoverty backgrounds. I conducted a document analysis of research in character education referring to methods of integrating character education skills into classroom practice. I identified character education programs that provide instruction in the areas of the emotional resources that Payne (2013) suggests that students from high-poverty backgrounds lack. Then, I made connections between how these identified character education skills align to the studio habits of mind (Hetland, 2013) that the visual arts have been suggested to develop in students to create guidelines for art educators to implement in their classrooms. INDEX WORDS: Urban art education, Low-income communities, High-poverty backgrounds, Character education, Grit, Self-Control, Optimism, Social intelligence GUIDELINES FOR TEACHING ART TO STUDENTS FROM URBAN HIGH-POVERTY BACKGROUNDS
A method for projecting useful life of LED lighting systems

This study investigated a non-invasive method to determine the junction temperature of AlGaInP light-emitting diodes (LEDs) in a system. Because the primary cause for the AlGaInP LED degradation is junction temperature, this method can be used to predict LED life. Currently, life estimates of LED lighting systems quoted by manufacturers (commonly 100,000 hours) are based on the average life of a single LED measured under specific laboratory conditions. In reality, rates of degradation are much different for LEDs in a system than for those in a laboratory environment because the packaging and the environmental conditions in which the system operates can affect LED performance. Current practices for estimation require time-consuming life tests to accurately predict the life of LEDs. Therefore, a rapid estimation method for LED life is needed. Based on previous studies, the authors chose to focus on the measurement of junction temperature and its relationship to LED degradation. The primary objective of this study was to verify that wavelength shift could be used to estimate accurately the junction temperature of 5mm epoxy encapsulated AlGaInP LEDs. In this study, the junction temperature was increased by changing the drive current while holding the ambient temperature surrounding the LED constant, and by changing the surrounding temperature while holding the drive current steady. Experimental results from this study showed that for commercial LEDs, peak wavelengths shift proportionally to junction temperature regardless of how the temperature is created at the junction, and that this linear relationship could be used as a direct measure of the junction temperature. Because the primary cause for the degradation of AlGaInP LEDs is junction heat, the light output degradation rate of these types of LEDs can be predicted by measuring the spectral shift. Therefore, LED systems can be evaluated without disassembly in their intended application.
Morpheme-Based Language Modeling for Arabic Lvcsr

In this paper, we concentrate on Arabic speech recognition. Taking advantage of the rich morphological structure of the language, we use morpheme-based language modeling to improve the word error rate. We propose a simple constraining method to rid the decoding output of illegal morpheme sequences. We report the results obtained for word and morpheme language models using medium (64 kw) and large (~800 kw) vocabularies, the morpheme LM obtaining an absolute improvement of 2.4% for the former and only 0.2% for the latter. The 2.4% gain surpasses previous gains for morpheme-based LMs for Arabic, and the large vocabulary runs represent the first comparative results for vocabularies of this size for any language. Finally, we analyze the performance of the morpheme LM on word OOV's
An FPGA-based performance evaluation of the AES block cipher candidate algorithm finalists

The technical analysis used in determining which of the potential Advanced Encryption Standard candidates was selected as the Advanced Encryption Algorithm includes efficiency testing of both hardware and software implementations of candidate algorithms. Reprogrammable devices such as field-programmable gate arrays (FPGAs) are highly attractive options for hardware implementations of encryption algorithms, as they provide cryptographic algorithm agility, physical security, and potentially much higher performance than software solutions. This contribution investigates the significance of FPGA implementations of the Advanced Encryption Standard candidate algorithms. Multiple architectural implementation options are explored for each algorithm. A strong focus is placed on high-throughput implementations, which are required to support security for current and future high bandwidth applications. Finally, the implementations of each algorithm will be compared in an effort to determine the most suitable candidate for hardware implementation within commercially available FPGAs.
A Research Agenda for Helminth Diseases of Humans: Social Ecology, Environmental Determinants, and Health Systems

In this paper, the Disease Reference Group on Helminth Infections (DRG4), established in 2009 by the Special Programme for Research and Training in Tropical Diseases (TDR), with the mandate to review helminthiases research and identify research priorities and gaps, focuses on the environmental, social, behavioural, and political determinants of human helminth infections and outlines a research and development agenda for the socioeconomic and health systems research required for the development of sustainable control programmes. Using Stockols' social-ecological approach, we describe the role of various social (poverty, policy, stigma, culture, and migration) and environmental determinants (the home environment, water resources development, and climate change) in the perpetuation of helminthic diseases, as well as their impact as contextual factors on health promotion interventions through both the regular and community-based health systems. We examine these interactions in regard to community participation, intersectoral collaboration, gender, and possibilities for upscaling helminthic disease control and elimination programmes within the context of integrated and interdisciplinary approaches. The research agenda summarises major gaps that need to be addressed.
Multilocus Sequence Typing Identifies Epidemic Clones of Flavobacterium psychrophilum in Nordic Countries

ABSTRACT Flavobacterium psychrophilum is the causative agent of bacterial cold water disease (BCWD), which affects a variety of freshwater-reared salmonid species. A large-scale study was performed to investigate the genetic diversity of F. psychrophilum in the four Nordic countries: Denmark, Finland, Norway, and Sweden. Multilocus sequence typing of 560 geographically and temporally disparate F. psychrophilum isolates collected from various sources between 1983 and 2012 revealed 81 different sequence types (STs) belonging to 12 clonal complexes (CCs) and 30 singleton STs. The largest CC, CC-ST10, which represented almost exclusively isolates from rainbow trout and included the most predominant genotype, ST2, comprised 65% of all isolates examined. In Norway, with a shorter history (<10 years) of BCWD in rainbow trout, ST2 was the only isolated CC-ST10 genotype, suggesting a recent introduction of an epidemic clone. The study identified five additional CCs shared between countries and five country-specific CCs, some with apparent host specificity. Almost 80% of the singleton STs were isolated from non-rainbow trout species or the environment. The present study reveals a simultaneous presence of genetically distinct CCs in the Nordic countries and points out specific F. psychrophilum STs posing a threat to the salmonid production. The study provides a significant contribution toward mapping the genetic diversity of F. psychrophilum globally and support for the existence of an epidemic population structure where recombination is a significant driver in F. psychrophilum evolution. Evidence indicating dissemination of a putatively virulent clonal complex (CC-ST10) with commercial movement of fish or fish products is strengthened.
APPLICATION OF DEEP UV RESONANCE RAMAN SPECTROSCOPY TO BIOPROCESSING

currently a relatively small percentage of conventional pharmaceuticals, continues to expand with predicted revenues of over USD 100 billion for 2010. With continual demand for high fidelity products, from recombinant therapeutic proteins to nucleic acid-based medicinal products, the need for reliable, cost effective and appropriate analytical techniques for assessing the conformity of the products is still paramount. Monitoring of these complex processes is important for accurate assessment of product yield and quality control, but is also necessary to gain a greater knowledge of both the chemical and physical changes that occur. Increased biological understanding of the cellular processes can further facilitate bioprocess design and ultimately improve both quality and quantity of the product, particularly if real-time and on-line information can be collected. The confocal nature of Raman spectroscopy and the fact that water has only a weak Raman scatter means that Raman measurements can be taken of solutions directly through transparent materials, such as the side of a reaction vessel. Furthermore, with continuing advancements in spectroscopic instrumentation reducing size and cost as well as improved software capabilities, Raman spectroscopy is extremely applicable to both on-line and real time monitoring. Just over a decade ago, Shaw et al. demonstrated that Raman spectroscopy could be successfully applied to the on-line monitoring of the biotransformation by yeast of glucose to ethanol. The results showed that with an appropriate on-line set-up and specifically designed software for data preprocessing and multivariate analysis, glucose and ethanol concentrations could be measured with over five per cent accuracy (compared to off-line chemical and enzymatic diagnostic methods). Further work, comparing a diverse range of unprocessed, industrial fed-batch fermentation broths containing the fungus Gibberella fujikuroi also successfully applied Raman spectroscopy and appropriate chemometric models to measure accurately the concentration of natural product gibberellic acid. Raman spectroscopy has also been used to evaluate the nature of particle contamination detecting micro-particles inside glass containers such as glass syringes, vials and test tubes. In recent years, Raman spectroscopy has been successfully applied to bioprocessing, including industrial processes. Raman studies have typically been aimed at measuring accurately both product yields and the presence of secondary products; including glucose and ethanol levels as well as secondary metabolites present in complex non-fractionated fermentation broths1,2. However, Raman spectroscopy as a tool for monitoring the complex structural changes occurring during protein production has to date been under utilised, particularly the use of the extremely sensitive structural technique of UV resonance Raman (UVRR) spectroscopy. APPLICATION OF DEEP UV RESONANCE RAMAN SPECTROSCOPY TO BIOPROCESSING
Conditional Gauss–Hermite Filtering With Application to Volatility Estimation

The conditional Gauss-Hermite filter (CGHF) utilizes a decomposition of the filter density by conditioning on an appropriate part of the state vector. In contrast to the usual Gauss-Hermite filter (GHF) it is only assumed that the terms in the decomposition can be approximated by Gaussians. Due to the nonlinear dependence on the condition, quite complicated densities can be modeled, but the advantages of the normal distribution are preserved. For example, in models with multiplicative noise occuring in Bayesian estimation, the joint density of state and variance parameter strongly deviates from a bivariate Gaussian, whereas the conditional density can be well approximated by a normal distribution. As in the GHF, integrals in the time and measurement updates are computed by Gauss-Hermite quadrature. Alternatively, the unscented transform can be used, leading to a conditional unscented Kalman filter (CUKF).
An interplay of the base excision repair and mismatch repair pathways in active DNA demethylation

Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC residues whilst avoiding generation of toxic BER intermediates and whether alternative DNA repair pathways participate in ADDM. It has been shown that non-canonical DNA mismatch repair (ncMMR) can remove both alkylated and oxidized nucleotides from DNA. Here, a phagemid DNA containing oxidative base lesions and methylated sites are used to examine the involvement of various DNA repair pathways in ADDM in murine and human cell-free extracts. We demonstrate that, in addition to short-patch BER, 5-hydroxymethyluracil and uracil mispaired with guanine can be processed by ncMMR and long-patch BER with concomitant removal of distant 5mC residues. Furthermore, the presence of multiple mispairs in the same MMR nick/mismatch recognition region together with BER-mediated nick formation promotes proficient ncMMR resulting in the reactivation of an epigenetically silenced reporter gene in murine cells. These findings suggest cooperation between BER and ncMMR in the removal of multiple mismatches that might occur in mammalian cells during ADDM.
Efficient mining of frequent sequence generators

Sequential pattern mining has raised great interest in data mining research field in recent years. However, to our best knowledge, no existing work studies the problem of frequent sequence generator mining. In this paper we present a novel algorithm, FEAT (abbr. Frequent sEquence generATor miner), to perform this task. Experimental results show that FEAT is more efficient than traditional sequential pattern mining algorithms but generates more concise result set, and is very effective for classifying Web product reviews.
Radiological Clinical Practice Guidelines Published in the Last Decade: A Bibliometric Analysis

Objectives: To provide a comprehensive review of radiological clinical practice guidelines (CPGs) and to establish their characteristics and impact in the field of radiology. Material and Methods: A MEDLINE search was performed for CPGs in which at least half of the authors were from the radiology or imaging department. The following information was extracted from each CPG: year of publication, journal, provider, number of authors, number of pages, number of references, collaboration, country of origin, radiological subspecialty, imaging modality used, topic, source of funding, and number and pattern of citations. Results: In total, 120 radiological CPGs published between July 2006 and June 2016 were identified. One hundred nine (90.8%) radiological CPGs were published in radiology journals, 96 (80.0%) were provided by the scientific community, 108 (90.0%) were collaborative studies, 64 (53.3%) originated from the United States, 36 (30.0%) were concerned with the field of vascular/interventional radiology, 38 (31.7%) used combined imaging techniques, 52 (43.3%) were focused on interpretation and management, and 118 (98.4%) were not funded. Radiological CPGs included a median of 8 authors, 9 pages, and 49 references. The median number of citations and annual citations were 18 (range, 0–540) and 3.5 (range, 0–75.6), respectively. Conclusion: Our study presents several interesting insights into the characteristics and impact of radiological CPGs.