bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrological and Morphological Changes of the Lower Danube Near Mohács, Hungary
Authors: Nagy Judit , Kiss Tímea 
Published: August 2016

Abstract
Various direct human impacts changed the hydro-morphology of the Danube during the last centuries. The aims of the present study are (1) to analyze the water regime of the Danube River using the data of Mohács gauging station (1900-2013), and (2) to study the channel development (1952-2014) in connection with water regime changes and human impacts at a section near Bogyiszló (upstream of Mohács). According to the results the height of low water stages decreased by approx. 136 cm (1.2 cm/year), and new, high record flood stages were measured too. The discharge values appertaining to the same low water stages doubled, thus nowadays almost twice as much water flows through the cross-section of the channel at a given stage as at the beginning of the studied period. As the duration of low stages increased, the sandbar development intensified, thus the channel became narrower (by 48% at some places) and deeper thalweg evolved. Therefore, a smaller cross-section for flood-waves evolved, affecting the height of flood. These changes affect shipping, as due to riverbed incision and decrease of low water stages, the lowest shipping water level has to be set repeatedly at lower stages. Besides water extraction from the channel will have difficulties, thus irrigation and industrial cooling water supply will be limited in the future.
Open Source Web GIS Solutions in Disaster Management – with Special Emphasis on Inland Excess Water Modeling
Authors: Juhász Levente , Podolcsák Ádám , Doleschall János 
Published: August 2016

Abstract
In recent years, the increased frequency of inland excess water in the Carpathian Basin gets more and more attention. The authors developed a web based pilot application for disaster management, with special emphasis on inland excess water hazard management. Free and open source software was used to generate a model, and our work was based on Web GIS standards (OGC), which makes further development possible. The developed Web GIS application provides functions to support the data collection regarding channels and ditches, and on-line hydrological analysis based on OGC Web Processing Services (WPS). Hydrological analysis aims to visualize the areas potentially at risk, depending on different precipitation quantities and various values of influencing factors. In order to run the prototype a sample data set was gathered including reference maps, technical parameters and current condition of canals and ditches. The methodology of crowdsourcing can produce valuable Volunteered Geographic Information (VGI) that can fulfill the data requirements of disaster management applications. The prototype supports Crowdsourcing in the following aspects: free user access to the system’s analysis functionality, stakeholders may digitize the position of ditches, modify the status of the existing ditch system according to current conditions and add or modify parameters relevant for the analysis. The application demonstrated the usability of stakeholder generated geographic information and web processing for disaster management. The idea of integrating user-generated data into the various tasks of a disaster management agency is promising. However, maintaining data quality and standards compliance remain important issues.
When soundscape meets architecture
Authors: Schulte-Fortkamp Brigitte , Jordan Pamela 
Published: August 2016

Abstract
The harmonization of noise indicators, noise
mapping, and action plans delivers basic administrative
information not only for noise abatement in highly noisepolluted
areas, but also for comparisons across built environments
regionally and internationally. However, such
activities do not provide any tools or essential knowledge
for the more demanding tasks required in designing and
planning sustainable built environments that are supportive
to wellbeing and health. Without knowing the determining
factors behind dose-response curves [1, 2], the decision
process for developing action plans is unnecessarily
restricted. Optional courses of action for handling a noise
problem cannot be sufficiently considered without understanding
the full context—physical, cultural, emotional—
of noise’s effect on people. Therefore, an approach for
considering these many angles must involve diverse fields
of practice and interdisciplinary approaches. One such
methodology is the multidimensional Soundscape Approach,
which emphasizes how the acoustic environment
is perceived, experienced, and/or understood by a person
or people in context. Relying on principles of the Soundscape
Approach, two urban green spaces will be examined
regarding noise abatement strategies in relation to visitors’
experiential expectations. It will be shown how and why
soundscape is an invaluable tool in detecting and analyzing
needs for an adequate acoustic environment, accounting
for people’s concerns and integrating their local expertise
to guide the process of planning, designing and maintaining
sites.
Partnership and Race in Mission Encounters in Tanzania
Authors: Christian Elaine Elisabeth 
Published: August 2016

Abstract
I examine racial and ethnic dynamics in encounters between Tanzanian church personnel,
and visiting American partners or short-term missionaries. Contemporary mission work in Tanzania is
situated within a historical context that includes, but is not ultimately determined by, race or ethnicity.
Several kinds of engagements and partnerships exist between American religious organisations and the
Tanzanian church, which I describe ethnographically, and discuss how encounters between Tanzanian
Christians and American visitors become ethnically inflected. Two cases—encounters with Maasai and
Chagga people respectively—provide a comparative illustration. Finally, I address the role played by
new types of partnership between Tanzanian and American religious organisations, and how themes of
hospitality and identities as guests and hosts contribute to encounters between American and Tanzanian
Christians. In these encounters, multiple areas of shifting meanings of race come together, resulting in
disjunctures of understanding. I suggest that these disjunctures, coupled with the guest-host dynamic
and the lack of in-depth knowledge characteristic of short-term mission in general, reveal patterns of
social inequality and tensions inherent in the changing context of Christian mission.
Characterization of a Single Genomic Locus Encoding the Clustered Protocadherin Receptor Diversity in Xenopus tropicalis
Authors: Etlioglu Hakki E , Sun Wei , Huang Zengjin , Chen Wei , Schmucker Dietmar 
Published: August 2016

Abstract
Clustered protocadherins (cPcdhs) constitute the largest subgroup of the cadherin superfamily, and in mammals are grouped into clusters of α-, β-, and γ-types. Tens of tandemly arranged paralogous Pcdh genes of the Pcdh clusters generate a substantial diversity of receptor isoforms. cPcdhs are known to have important roles in neuronal development, and genetic alterations of cPcdhs have been found to be associated with several neurological diseases. Here, we present a first characterization of cPcdhs in Xenopus tropicalis. We determined and annotated all cPcdh isoforms, revealing that they are present in a single chromosomal locus. We validated a total of 96 isoforms, which we show are organized in three distinct clusters. The X. tropicalis cPcdh locus is composed of one α- and two distinct γ-Pcdh clusters (pcdh-γ1 and pcdh-γ2). Bioinformatics analyses assisted by genomic BAC clone sequencing showed that the X. tropicalis α- and γ-Pcdhs are conserved at the cluster level, but, unlike mammals, X. tropicalis does not contain a β-Pcdh cluster. In contrast, the number of γ-Pcdh isoforms has expanded, possibly due to lineage-specific gene duplications. Interestingly, the number of X. tropicalis α-Pcdhs is identical between X. tropicalis and mouse. Moreover, we find highly conserved as well as novel promoter elements potentially involved in regulating the cluster-specific expression of cPcdh isoforms. This study provides important information for the understanding of the evolutionary history of cPcdh genes and future mechanistic studies. It provides an annotated X. tropicalis cPcdh genomic map and a first molecular characterization essential for functional and comparative studies.
Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium
Authors: Wall Jeffrey D , Stevison Laurie S 
Published: August 2016

AbstractWith recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations.
Comparative Analysis of Regions with Distorted Segregation in Three Diploid Populations of Potato
Authors: Manrique-Carpintero Norma C , Coombs Joseph J , Veilleux Richard E , Buell C Robin , Douches David S 
Published: August 2016

AbstractGenes associated with gametic and zygotic selection could underlie segregation distortion, observed as alterations of expected Mendelian genotypic frequencies in mapping populations. We studied highly dense genetic maps based on single nucleotide polymorphisms to elucidate the genetic nature of distorted segregation in potato. Three intra- and interspecific diploid segregating populations were used. DRH and D84 are crosses between the sequenced doubled monoploid DM 1-3 516 R44 Solanum tuberosum Group Phureja and either RH89-039-16 S. tuberosum or 84SD22, a S. tuberosum × S. chacoense hybrid. MSX902 is an interspecific cross between 84SD22 and Ber83 S. berthaultii × 2 × species mosaic. At the 0.05 significance level, 21%, 57%, and 51% of the total markers mapped in DRH, D84, and MSX902 exhibited distorted segregation, respectively. Segregation distortion regions for DRH were located on chromosomes 9 and 12; for D84 on chromosomes 2, 3, 4, 6, 7, and 8; and on chromosomes 1, 2, 7, 9, and 12 for MSX902. In general, each population had unique segregation distortion regions and directions of distortion. Interspecific crosses showed greater levels of distorted segregation and lower recombination rates as determined from the male parents. The different genomic regions where the segregation distortion regions occurred in the three populations likely reflect unique genetic combinations producing distorted segregation.
Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae
Authors: Cui Ping , Jin Huiyan , Vutukuru Manjula Ramya , Kaplan Craig D 
Published: August 2016

Abstract
The interplay between adjacent transcription units can result in transcription-dependent alterations in chromatin structure or recruitment of factors that determine transcription outcomes, including the generation of intragenic or other cryptic transcripts derived from cryptic promoters. Mutations in a number of genes in Saccharomyces cerevisiae confer both cryptic intragenic transcription and the Suppressor of Ty (Spt-) phenotype for the lys2-128∂ allele of the LYS2 gene. Mutants that suppress lys2-128∂ allow transcription from a normally inactive Ty1 ∂ promoter, conferring a LYS+ phenotype. The arrangement of transcription units at lys2-128∂ is reminiscent of genes containing cryptic promoters within their open reading frames. We set out to examine the relationship between RNA Polymerase II (Pol II) activity, functions of Spt elongation factors, and cryptic transcription because of the previous observation that increased-activity Pol II alleles confer an Spt- phenotype. We identify both cooperating and antagonistic genetic interactions between Pol II alleles and alleles of elongation factors SPT4, SPT5, and SPT6. We find that cryptic transcription at FLO8 and STE11 is distinct from that at lys2-128∂, though all show sensitivity to reduction in Pol II activity, especially the expression of lys2-128∂ found in Spt- mutants. We determine that the lys2-128∂ Spt- phenotypes for spt6-1004 and increased activity rpo21/rpb1 alleles each require transcription from the LYS2 promoter. Furthermore, we identify the Ty1 transcription start site (TSS) within the ∂ element as the position of Spt- transcription in tested Spt- mutants.
A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification
Authors: Fulop Daniel , Ranjan Aashish , Ofner Itai , Covington Michael F , Chitwood Daniel H , West Donelly , Ichihashi Yasunori , Headland Lauren , Zamir Daniel , Maloof Julin N , Sinha Neelima R 
Published: August 2016

AbstractQuantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.
Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea
Authors: Lakshmanan Vairavan , Bansal Dhiru , Kulkarni Jahnavi , Poduval Deepak , Krishna Srikar , Sasidharan Vidyanand , Anand Praveen , Seshasayee Aswin , Palakodeti Dasaradhi 
Published: August 2016

Abstract
In eukaryotes, 3′ untranslated regions (UTRs) play important roles in regulating posttranscriptional gene expression. The 3′UTR is defined by regulated cleavage/polyadenylation of the pre-mRNA. The advent of next-generation sequencing technology has now enabled us to identify these events on a genome-wide scale. In this study, we used poly(A)-position profiling by sequencing (3P-Seq) to capture all poly(A) sites across the genome of the freshwater planarian, Schmidtea mediterranea, an ideal model system for exploring the process of regeneration and stem cell function. We identified the 3′UTRs for ∼14,000 transcripts and thus improved the existing gene annotations. We found 97 transcripts, which are polyadenylated within an internal exon, resulting in the shrinking of the ORF and loss of a predicted protein domain. Around 40% of the transcripts in planaria were alternatively polyadenylated (ApA), resulting either in an altered 3′UTR or a change in coding sequence. We identified specific ApA transcript isoforms that were subjected to miRNA mediated gene regulation using degradome sequencing. In this study, we also confirmed a tissue-specific expression pattern for alternate polyadenylated transcripts. The insights from this study highlight the potential role of ApA in regulating the gene expression essential for planarian regeneration.
Accumulation of Deleterious Mutations Near Sexually Antagonistic Genes
Authors: Connallon Tim , Jordan Crispin Y 
Published: August 2016

AbstractMutation generates a steady supply of genetic variation that, while occasionally useful for adaptation, is more often deleterious for fitness. Recent research has emphasized that the fitness effects of mutations often differ between the sexes, leading to important evolutionary consequences for the maintenance of genetic variation and long-term population viability. Some forms of sex-specific selection—i.e., stronger purifying selection in males than females—can help purge a population’s load of female-harming mutations and promote population growth. Other scenarios—e.g., sexually antagonistic selection, in which mutations that harm females are beneficial for males—inflate genetic loads and potentially dampen population viability. Evolutionary processes of sexual antagonism and purifying selection are likely to impact the evolutionary dynamics of different loci within a genome, yet theory has mostly ignored the potential for interactions between such loci to jointly shape the evolutionary genetic basis of female and male fitness variation. Here, we show that sexually antagonistic selection at a locus tends to elevate the frequencies of deleterious alleles at tightly linked loci that evolve under purifying selection. Moreover, haplotypes that segregate for different sexually antagonistic alleles accumulate different types of deleterious mutations. Haplotypes that carry female-benefit sexually antagonistic alleles preferentially accumulate mutations that are primarily male harming, whereas male-benefit haplotypes accumulate mutations that are primarily female harming. The theory predicts that sexually antagonistic selection should shape the genomic organization of genetic variation that differentially impacts female and male fitness, and contribute to sexual dimorphism in the genetic basis of fitness variation.
Transcriptome Profiling IdentifiesMultiplexinas a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance DuringDrosophilaVisual Development
Authors: Ma Jingqun , Brennan Kaelan J , D’Aloia Mitch R , Pascuzzi Pete E , Weake Vikki M 
Published: August 2016

AbstractThe Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex is a transcriptional coactivator with histone acetylase and deubiquitinase activities that plays an important role in visual development and function. In Drosophila melanogaster, four SAGA subunits are required for the deubiquitination of monoubiquitinated histone H2B (ubH2B): Nonstop, Sgf11, E(y)2, and Ataxin 7. Mutations that disrupt SAGA deubiquitinase activity cause defects in neuronal connectivity in the developing Drosophila visual system. In addition, mutations in SAGA result in the human progressive visual disorder spinocerebellar ataxia type 7 (SCA7). Glial cells play a crucial role in both the neuronal connectivity defect in nonstop and sgf11 flies, and in the retinal degeneration observed in SCA7 patients. Thus, we sought to identify the gene targets of SAGA deubiquitinase activity in glia in the Drosophila larval central nervous system. To do this, we enriched glia from wild-type, nonstop, and sgf11 larval optic lobes using affinity-purification of KASH-GFP tagged nuclei, and then examined each transcriptome using RNA-seq. Our analysis showed that SAGA deubiquitinase activity is required for proper expression of 16% of actively transcribed genes in glia, especially genes involved in proteasome function, protein folding and axon guidance. We further show that the SAGA deubiquitinase-activated gene Multiplexin (Mp) is required in glia for proper photoreceptor axon targeting. Mutations in the human ortholog of Mp, COL18A1, have been identified in a family with a SCA7-like progressive visual disorder, suggesting that defects in the expression of this gene in SCA7 patients could play a role in the retinal degeneration that is unique to this ataxia.
Prospects of Genomic Prediction in the USDA Soybean Germplasm Collection: Historical Data Creates Robust Models for Enhancing Selection of Accessions
Authors: Jarquin Diego , Specht James , Lorenz Aaron 
Published: August 2016

Abstract
The identification and mobilization of useful genetic variation from germplasm banks for use in breeding programs is critical for future genetic gain and protection against crop pests. Plummeting costs of next-generation sequencing and genotyping is revolutionizing the way in which researchers and breeders interface with plant germplasm collections. An example of this is the high density genotyping of the entire USDA Soybean Germplasm Collection. We assessed the usefulness of 50K single nucleotide polymorphism data collected on 18,480 domesticated soybean (Glycine max) accessions and vast historical phenotypic data for developing genomic prediction models for protein, oil, and yield. Resulting genomic prediction models explained an appreciable amount of the variation in accession performance in independent validation trials, with correlations between predicted and observed reaching up to 0.92 for oil and protein and 0.79 for yield. The optimization of training set design was explored using a series of cross-validation schemes. It was found that the target population and environment need to be well represented in the training set. Second, genomic prediction training sets appear to be robust to the presence of data from diverse geographical locations and genetic clusters. This finding, however, depends on the influence of shattering and lodging, and may be specific to soybean with its presence of maturity groups. The distribution of 7608 nonphenotyped accessions was examined through the application of genomic prediction models. The distribution of predictions of phenotyped accessions was representative of the distribution of predictions for nonphenotyped accessions, with no nonphenotyped accessions being predicted to fall far outside the range of predictions of phenotyped accessions.
Identification of Functional Domains in the Cohesin Loader Subunit Scc4 by a Random Insertion/Dominant Negative Screen
Authors: Shwartz Michal , Matityahu Avi , Onn Itay 
Published: August 2016

Abstract
Cohesin is a multi-subunit complex that plays an essential role in genome stability. Initial association of cohesin with chromosomes requires the loader—a heterodimer composed of Scc4 and Scc2. However, very little is known about the loader’s mechanism of action. In this study, we performed a genetic screen to identify functional domains in the Scc4 subunit of the loader. We isolated scc4 mutant alleles that, when overexpressed, have a dominant negative effect on cell viability. We defined a small region in the N terminus of Scc4 that is dominant negative when overexpressed, and on which Scc2/Scc4 activity depends. When the mutant alleles are expressed as a single copy, they are recessive and do not support cell viability, cohesion, cohesin loading or Scc4 chromatin binding. In addition, we show that the mutants investigated reduce, but do not eliminate, the interaction of Scc4 with either Scc2 or cohesin. However, we show that Scc4 cannot bind cohesin in the absence of Scc2. Our results provide new insight into the roles of Scc4 in cohesin loading, and contribute to deciphering the loading mechanism.