Miracle-dz/UniFAR-FTUs huggingface dataset:
Journal of Environmental Quality MicrobiAl WAter QuAlity — Monitoring And Modeling SpeciAl Section core ideas

Increases in swine production and concomitant manure application provide beneficial nutrients for crops but also include the potential to spread pathogenic bacteria in the environment. While manure is known to contain a variety of pathogens, little is known regarding the long-term effect of manure application on fate and transport of this diverse set of pathogens into surrounding waterways. We report on the use of 16S-rRNA gene sequencing to detect pathogen-containing genera in the agriculturally dominated South Fork Iowa River watershed, home to approximately 840,000 swine in the 76,000-ha basin. DNA was extracted from monthly grab samples collected from three surface water sites and two main artificial drainage outlets. DNA sequences from water samples were matched with sequences from genera known to contain pathogens using targeted 16S rRNA amplicon sequencing. The specific genera known to contain pathogens were quantified by combining percentage of genera sequence matches with 16S rRNA gene quantitative polymerase chain reaction results. Specifically, abundances of Bacteroides, Clostridium sensu stricto, and Acinetobactersignificantly increased in surface water after typical fall manure application. Additionally, the likely transport pathways for specific genera known to contain pathogens were identified. Surface water Enterobacter concentrations were influenced mainly by artificial drainage, whereas Clostridium sensu stricto was primarily transported to surface waters by runoff events. The results of this study will help us to understand environmental pathways that may be useful for mitigation of the diverse set of pathogenic genera transported in agroecosystems and the capability of manure application to alter existing microbial community structures.
Vision Assisted Navigation for Miniature Unmanned Aerial Vehicles (MAVs)

One of the primary difficulties in flying airplanes of all sizes is navigation, or ensuring that the location and attitude of the airplane is known at all times. For large aerial systems, high-quality IMUs have been successfully used for decades. However, the weight, power, cost, and size restrictions of miniature-UAVs (MAVs) preclude the use of high-quality IMUs for navigation. For the past two and a half years, this contract has enabled the investigation of techniques for enabling high-quality navigation using a combination of lowquality inertial sensors, visual sensors, and (when available) GPS. Specific areas of contribution from this project include: (1) real-time techniques for improving pose estimates on MAVs with GPS, (2) two proposed approaches for enabling GPS-denied navigation, (3) quantitative and analytical analyses of different navigation algorithms, and (4) GPS-denied navigation utilizing multiple agents. The contributions in each of these areas is discussed in this report.
University of Groningen Focus on Membrane Differentiation and Membrane Domains in the Prokaryotic Cell Boekema

A summary is presented of membrane differentiation in the prokaryotic cell, with an emphasis on the organization of proteins in the plasma/cell membrane. Many species belonging to the Eubacteria and Archaea have special membrane domains and/or membrane proliferation, which are vital for different cellular processes. Typical membrane domains are found in bacteria where a specific membrane protein is abundantly expressed. Lipid rafts form another example. Despite the rareness of conventional organelles as found in eukaryotes, some bacteria are known to have an intricate internal cell membrane organization. Membrane proliferation can be divided into curvature and invaginations which can lead to internal compartmentalization. This study discusses some of the clearest examples of bacteria with such domains and internal membranes. The need for membrane specialization is highest among the heterogeneous group of bacteria which harvest light energy, such as photosynthetic bacteria and halophilic archaea. Most of the highly specialized membranes and domains, such as the purple membrane, chromatophore and chlorosome, are found in these Published online: August 5, 2013 Egbert J. Boekema Department of Electron Microscopy Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, NL–9747 AG Groningen (The Netherlands) E-Mail e.j.boekema @ rug.nl © 2013 S. Karger AG, Basel 1464–1801/13/0235–0345$38.00/0
1 7-Methylguanosine modifications in tRNA 2

More than 90 different modified nucleosides have been identified in tRNA. Among the 8 tRNA modifications, the 7-methylguanosine (m7G) modification is found widely in eubacteria, 9 eukaryotes, and a few archaea. In most cases, the m7G modification occurs at position 46 in the 10 variable region and is a product of tRNA (m7G46) methyltransferase. The m7G46 modification forms 11 a tertiary base pair with C13-G22, and stabilizes the tRNA structure. Recently, we have proposed a 12 reaction mechanism for eubacterial tRNA m7G methyltransferase (TrmB) based on the results of 13 biochemical studies and previous biochemical, bioinformatic, and structural studies by others. 14 However, an experimentally determined mechanism of methyl-transfer remains to be ascertained. 15 The physiological functions of m7G46 in tRNA have started to be determined over the past decade. 16 To be able to better respond to diseases and infections in which the m7G modification is considered 17 to be involved, it is still necessary to further understand the catalytic mechanism of AdoMet and/or 18 the tRNA bound form of m7G methyltransferases. In this review, information of tRNA m7G 19 modifications and tRNA m7G methyltransferases are summarized and the differences in reaction 20 mechanism between tRNA m7G methyltransferase and rRNA or mRNA m7G methylation enzyme 21 are discussed. 22
Obscured clusters - III. Follow-up observations of Mercer 23

Context. New infrared surveys have revealed over 1000 new open cluster candidates in the Milky Way, but these candidates need to be confirmed with follow up observations. Of particular interest are young, massive star clusters because they serve as nearby analogues to the distant super star clusters studied as point sources in other galaxies. Aims. We determine the physical parameters and investigate the high-mass stellar content of the infrared star cluster Mercer 23, situated near the Galactic plane (l = 53. ◦ 772, b =+ 0. ◦ 164). Methods. Our analysis is based on new Baade/PANIC JHKS and ISAAC/VLT imaging of Mercer 23 and ISAAC/VLT moderate resolution (R ≈ 4000) spectroscopy of the brightest cluster members in the H -a ndK-bands. The cluster age is determined from isochrone main-sequence (MS) and pre-MS fitting. We derive stellar parameters for eight of the stellar members, using a full non-LTE modeling of the obtained spectra. Results. Mercer 23 is a very young cluster, with age of t = 2–4 Myr. The cluster suffers reddening of E(J−KS) = 1.35, AV = 7. 2m ag. The derived distance is d = 6.5 ± 0.3 kpc. Our spectral modeling allows us to conclude that the three most luminous member are evolved highly massive stars: a WR star, and two mid-O supergiant stars, based on their derived luminosity. Conclusions. Mercer 23 is not a super-massive cluster such as those recently recognized to exist in the Milky Way. However, its mass
Areal texture and angle measurements of tilted surfaces using focus variation methods

Optical instruments for areal surface topography measurement have seen significant commercial development in the last five years, along with the ISO 25178 areal standard. Providing the user with confidence in new instruments depends on understanding instrument behavior and sources of error. Focus variation techniques rely on the inherent micro- or nano-scale roughness of a surface to allow acquisition of topography data. The work reported here has been examining the sensitivity of the focus variation technique to surface slope, using areal parameters to characterize surface roughness at extended slope values. The results illustrate links between instrument variables and slope characterization.
The incorporation of alkalis in beryl; a multinuclear MAS NMR and crystal-structure study

The stereochemical details of the incorporation of alkali ions into the beryl structure axe examined by multi-nuclear MAS NMR spectroscopy and single*rystal structure refinement. The 2eSi signal is narrow in alkali-poor beryl, and broadens with increasing alkali content, a result of the different short-range next-n€arest-neighbor configurations produced by the incorporation of alkalis into the structnre; we designate this substitutional broadening, and calculate its value from the proposed local configurations and the method of Sherriff & Grundy (1988). Substitutional broadening is observed in the 27AI spectra that also show only [6]-coordinate Al to be present, in agreement with the current and earlier X-ray results. Two 7Li signals are observed, indicating that Li occurs both as a framework constituent and as a channel species. The crystal structures of the four samples were refined, to R indices of 2-390 using MoKcr X radiation, The distance expands linearly with increasing Li :+ Be substitution at this site, but the O-Be-O bond angles remain unchanged. This substitution produces a bond-valence deficiency at the O(2) anion. This is compensated by lengthening of Si-O(l) and Si-O(l)a, and contraction of Si-O(2) with increasing Li + Be substitution. All samples of alkali-bearing beryl examined show residual electron density in the channels due to occupancy by alkali ions; all show more density at the 2a site than at the 2b site. Comparison of these residual densities with known alkali contents confinns previous work tlut assigned Cs to the 2a position. The electron density observed at the 2b position correlates well with the Na contents and is iniufficient to account for the H2O; thu$ we assign Na to 2b and H2O to 24. Local stereochemistry and analytical rerults suggest tlat Na is bonded to two H2O groups in the channel.
Regression Levels of Selected Affective Factors on Science Achievement: A Structural Equation Model with TIMSS 2011 Data

The aim of this study is to demonstrate the science success regression levels of chosen emotional features of elementary 8th grade students using Structural Equation Model. The study was conducted by the analysis of students’ questionnaires and science success in TIMSS 2011 data using SEM. Initially, the factors that are thought to have an effect on science success were detected out of TIMSS questionnaire and KMO and Bartlett’s tests were done to test appropriateness of these items to factor analysis. Explanatory Factor analysis was done for the sub-dimensions that were seen to be suitable for factor analysis and then, confirmative factor analysis was done using LISREL and the appropriateness of dimensions to the model was tested. Seeing that the concordance indexes od dimensions were suitable to the model, structural model was rested. At the end of the SEM test, it was found that the attitudes and values of 8th grade students predicted their science success in a positive way, and negative attitudes and their self-confidence predicted their success in a negative way.
Identifying the key genes and microRNAs in colorectal cancer liver metastasis by bioinformatics analysis and in vitro experiments

Colorectal cancer (CRC) is one of the principal causes of cancer-associated mortality worldwide. The high incidence of liver metastasis is the leading risk factor of mortality in patients with CRC, and the mechanisms of CRC liver metastasis are poorly understood. In the present study, 7 datasets, including 3 gene expression profile datasets and 4 microRNA (miRNA) expression profile datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) database to identify potential key genes and miRNAs, which may be candidate biomarkers for CRC liver metastasis. Differentially expressed (DE) genes (DEGs) and DE miRNAs of primary CRC tumor tissues and liver metastatic CRC tumor tissues were selected using the GEO2R tool. Gene Ontology and Kyoto Encyclopedia of Gene and Genome pathway enrichment analyses were conducted using the Database for Annotation, Visualization and Integrated Discovery online database. Furthermore, Cytoscape with cytoHubba and the Molecular Complex Detection (MCODE) plug-in were used to visualize a protein-protein interaction (PPI) network for these DEGs, and to screen hub genes and gene modules in the PPI network. In addition, the online databases, TargetScan, miRanda, PITA, miRWalk and miRDB, were used to identify the target genes of the DE miRNAs. In the present study, 141 DEGs (97 upregulated and 44 downregulated) and 3 DE miRNAs (2 upregulated and 1 downregulated) were screened from the 3 gene expression microarray datasets and 4 miRNA expression microarray datasets, respectively. In total, 10 hub genes with a high degree of connectivity were selected from the PPI network, including albumin (ALB), coagulation factor II (F2), thrombin, apolipoprotein H (APOH), serpin family C member 1 (SERPINC1), apolipoprotein A1 (APOA1), α-1-microglobulin/bikunin precursor (AMBP), apolipoprotein C3 (APOC3), plasminogen (PLG), α-2 HS glycoprotein (AHSG) and apolipoprotein B (APOB). The most important module was detected in the PPI network using the MCODE plug-in. A total of 20 DEGs were identified to be potential target genes of these DE miRNAs, and novel miRNA-DEGs regulatory axes were constructed. In vitro experiments were performed to demonstrate that miR-885 promoted CRC cell migration by, at least partially, decreasing the expression of von Willebrand factor (vWF) and insulin-like growth factor binding protein 5 (IGFBP5). In conclusion, by using integrated bioinformatics analysis and in vitro experiments, key candidate genes were identified and novel miRNA-mRNA regulatory axes in CRC liver metastasis were constructed, which may improve understanding of the molecular mechanisms underlying CRC liver metastasis.
Title A comprehensive framework for prioritizing variants in exomesequencing studies of Mendelian diseases

Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate variants in the proof-of-concept examples. The proposed framework, implemented in a user-friendly software package, named KGGSeq (http://statgenpro.psychiatry.hku.hk/kggseq), will play a very useful role in exome sequencing-based discovery of human Mendelian disease genes.
Biodegredation of Different Agro-Endustrial Wastes through the Cultivation of Pleurotus ostreatus (Jacq. ex. Fr) Kummer

The aim of this study was to investigate the effect of various substrates on spawn running time, yield and biological efficiency (BE) of Pleurotus ostreatus (Jacq. ex. Fr) , compositional changes of substrates after growth mushroom and to evaluate its potential use as a feedstock. In the study, chickpea straw (CS) was used as basal substrate (80 %), while some of agricultural wastes such as cotton seed hulls (CSH), olive press cake (OPC), sunflower seed press cake (SPC) and sugar beet pulp (SBP) were added at the rate of 20 % to basal substrate. It was determinated that all of agricultural wastes tested in the study, except SBP, are economically viable alternatives for P. ostreatus (Jacq. ex. Fr) growers. On the other hand, the increment in ash, N, P, K, Mg, Fe and Mn content and the decrease in moisture, pH, C, C:N, Zn and Cu, cellulose, hemicellulose and lignin content of substrates were observed after mushroom production. According to this results, we can suggest that CSH, OPC and SPC can be used as a additive material for P. ostreatus (Jacq. ex. Fr) cultivation and spent mushroom substrates may be a valuable material as a feedstock, because of higher nutritional content and digestibility.
The concept of terroir : The elusive cultural elements as defined by the Central Otago Wine Region

The impact of the physiological elements of terroir, soil, climate, and topography on the taste of wine is well accepted in wine research. Less research has been conducted on the cultural interposition of man concerning tradition, environmental orientation, and information and social exchange within wine regions in enhancing terroir. In spite of deficiency in the literature concerning the cultural elements of terroir, scholars suggest that they are of equal importance to the physiological elements in the concept of terroir. Because terroir is a distinctive marker of wine quality, terroir matters to consumers purchasing premium wines. Therefore, to provide a holistic delineation of terroir absent in the literature, this qualitative study defines the physiological and cultural elements of terroir for a particular wine region, the Central Otago Wine Region in the South Island of New Zealand, a New World wine region. The study was conducted through personal interviews with 24 vinters, viticulutralists, and managers associated with the wineries of the region. The findings demystified the cultural meaning of terroir as delineated by the regional constituents. The results are important to academia as it expands the literature on terroir and wine marketing. For practicum, the findings are advantageous for other regions striving to differentiate their wines in a decidedly competitive global marketplace.
Selecting 'interesting' scenarios with which to analyze policy response to potential climate change

The interactive complexity of the sources and effects of global climate change make it nearly impossible to analyze adaptive and/or abatement response stategies across the full range of possible futures. Researchers are therefore left to investigate their options along a few 'interesting' scenarlos of what the future 'might' hold, and so they must focus early attention upon how to select those scenarlos Two selection metrics are examined here. One, based upon minimizing the subjective mean squared error of when some critical state variable (or vector of variables) might cross a response threshold, has ~ t s roots in elementary statistical theory; but it is purely a physical measure. A second criterion, based upon min~m~zing the subjective expected cost of responding at such a threshold, has the advantage of incorporating these costs into the selection process. Subsequent analysis of the potential beneflts of abatement along scenarios selected in application of the second metric can thereby incorporate a reflect~on of efficient adaptation a first step towards seeing how to strike an appropriate balance between adaptation and abatement.
Conversational Characters that Support Interactive Play and Learning for Children

Over the last decade, digital technology has been increasingly used for educational purposes. The rationale behind this emerging trend is the belief that information technology can be utilized as a powerful means to assist learners with the acquisition of general knowledge, literacy, narrative competence, social skills like teamwork and negotiation capabilities, logical and spatial reasoning, eye-hand coordination and fine motor control, etc. In particular computer games and interactive technology have attracted a great deal of attention and much active research is currently being carried out in an effort to investigate their possible benefits in education (Squire, 2005). In this paper, we report on the development and evaluation of an educational agent architecture that allows for instructive communication and natural human-computer interaction between humans, in particular children and adolescents, and embodied historical characters. Our e-learning software platform is built around a three-dimensional animated portrayal of the world famous writer Hans Christian Andersen. Users can interact with the graphical character through a combination of speech, (pen and/or mouse) gesture, and keyboard and, in so doing, ask the virtual character questions about Andersen’s life, family, historical background, fairy tales and stories. The avatar is endowed with basic affective and emotional capabilities, and uses both synthesized speech and gestures to converse with the pupils. The intent of the system is educational while the interactive nature of the character is designed to help children learn and retain information about the subject matter to a greater extent than would be possible with traditional media. The educational content is pervasive for it is blended within the game-like system interface. In fact, there is no clear cut distinction between the system and the educational content which is always presented in different ways according to the conversational situation thus providing children with new opportunities for effective, immersive and rewarding computer-aided learning experiences. Conceptually, our system is backed by theories of user-centered learning as well as cognition. The constructivist theory of education (Mantovani, 2001) that recognizes the importance of active experience of students with the learning material supports our approach to education. Findings in the theory of multimedia learning (Mayer, 2001) that O pe n A cc es s D at ab as e w w w . in te ch w eb . o rg
In Vivo 3 T Magnetic Resonance Imaging Using a Biologically Specific Contrast Agent for Prostate Cancer : A Nude Mouse Model

We characterized in vivo a functional superparamagnetic iron-oxide magnetic resonance contrast agent that shortens the T2 relaxation time in magnetic resonance imaging (MRI) of prostate cancer xenografts. The agent was developed by conjugating Molday ION carboxyl-6 (MIC6), with a deimmunized mouse monoclonal antibody (muJ591) targeting prostate-specific membrane antigen (PSMA). This functional contrast agent could be used as a noninvasivemethod to detect prostate cancer cells that are PSMA positive and more readily differentiate them from surrounding tissues for treatment. The functional contrast agent was injected intravenously into mice and its effect was compared to both MIC6 (without conjugated antibody) and phosphate-buffered saline (PBS) injection controls. MR imaging was performed on a clinical 3T MRI scanner using a multiecho spin echo (MESE) sequence to obtain T2 relaxation time values. Inductively coupled plasma atomic emission spectroscopy was used to confirm an increase in elemental iron in injected mice tumours relative to controls. Histological examination of H&E stained tissues showed normal morphology of the tissues collected.