bluuebunny/crossref_metadata_2025 huggingface dataset:
THE STRUCTURAL ANALYSIS OF STEEL SILOS WITH CYLINDRICAL-WALL BEARING AND PROFILE-STEEL BEARING
Authors: Tang Zhengjun , Zhou Daibiao , Peng Chenwei , Wu Wenping
Published: November 2015

The silos are widely used in bulk material in many fields such as agriculture, mining, chemical, electric power storage, etc. Thin metal cylindrical silo shells are vulnerable to buckling failure caused by the compressive wall friction force. In this paper, the structural analysis of two types of steel silo with cylindrical-wall bearing and profile-steel bearing is implemented by Abaqus finite element analysis. The results indicate that under the same loading conditions, steel silos with profile-steel bearing and cylindrical-Wall bearing have similar values in Mises stress, but the steel silo with profile-steel bearing has a smaller radial displacement and a better capability of buckling resistance. Meanwhile, the total steel volumes reduced 8.0% comparing to the steel silo with cylindrical-wall bearing. Therefore, steel soil with profile-steel bearing not only has a less steel volumes but also a good stability.
Influence of newly synthesized imidazolium ionic liquids on activated sludge process
Authors: Gendaszewska Dorota , Liwarska-Bizukojć Ewa , Maton Cedric , Stevens Christian V.
Published: November 2015

This study investigates the influence of four imidazolium ionic liquids (ILs) present in wastewater on the activated sludge process. In addition, experiments with inactivated sludge to assess the capacity of this sorbent to remove ILs from the wastewater were conducted. It occurred that the presence of ionic liquids in wastewater reduces biomass growth and size of the sludge flocs. The strongest effect has been found for IL 6 (1-hexyl-2H-3-methyl-4,5-dimethylimidazolium iodide) with the longest alkyl chain length. Also, the degree of ILs removal increases with the alkyl chain length and decreases with the increase of initial concentration of ILs in wastewater. IL 6 reaches the highest degree of ILs removal from wastewater but inhibits the biomass growth and growth of sludge flocs in a greater extent than other tested compounds. Moreover, it was confirmed that newly synthesized ionic liquids can be adsorbed onto inactivated sludge. IL 6 could be adsorbed in a higher degree than other ionic liquids. This adsorption was described by Langmuir isotherm, whereas adsorption of other ionic liquids was described by Freundlich isotherm.
A long-term influence of anthropogenic alkalization on molluscs biodiversity in an area affected by cement industry, Świętokrzyskie Mountains, South-Central Poland
Authors: Barga-Więcławska Jadwiga Anna , Świercz Anna
Published: November 2015

The presented paper reports data from malacological and pedological studies carried out at sites representing diverse biotopes (beech wood, coniferous forest, and meadow) located 2 km away from the Dyckerhoff Cement Plant in Sitkówka-Nowiny in 1992 and in 2008–2009. The studies aimed to determine physicochemical properties of soils exposed to cement and limestone dust emission and to identify composition of snail communities inhabiting three different biotopes in relation to physicochemical properties of soils, and to grasp the dynamics of the alkalization-dependent changes in physicochemical properties of soils and their impact on the composition and ecological structure of malacofauna.
Stabilization and solidification of electric arc furnace dust originating from steel industry by using low grade MgO
Authors: Bayraktar Ahmet Can , Avşar Edip , Toröz İsmail , Alp Kadir , Hanedar Asude
Published: November 2015

In this study, solidification/stabilization (S/S) of electric arc furnace dust (EAFD) which is generated during the production of steel from scrap metals and classified as hazardous waste were investigated by using different ratios of cement and low grade MgO (LG MgO) as binding agents. Type I PC 42.5 R portland cement and LG MgO which contains 70–80% MgO were used. S/S blocks that contain different ratios of binding agents which have 1/0.5 – 1/1 – 1/2 – 1/3 – 1/4 – 1/5 cement/LG MgO ratio and S/S blocks which contain only cement and no LG MgO agents were prepared. These blocks, which contain 3 different waste ratios according to weight, 20%, 30% and 40% respectively, were produced and exposed to 28-day water purification. At the end of the purification process, S/S blocks were extracted using TCLP (Toxicity Characteristic Leaching Procedure) tests in order to determine the leaching behavior of Zn, Pb, and Cd in S/S blocks. By the end of this study, it was concluded that the recovery of EAFD is possible and applicable by immobilization. The findings of the study concluded that environmental performances or structural properties of blocks contain 30% waste by weight are suitable. This method is a proper one for recovering and treatment of EAFD with mixture of cement and LG MgO.
Spatial distribution and risk assessment of heavy metals in bottom sediments of two small dam reservoirs (south-east Poland)
Authors: Smal Halina , Ligęza Sławomir , Wójcikowska-Kapusta Anna , Baran Stanisław , Urban Danuta , Obroślak Radomir , Pawłowski Artur
Published: November 2015

Sediments of two dam reservoirs in SE Poland, Zalew Zemborzycki (ZZ) and Brody Iłżeckie (BI) were studied. The sediments from both reservoirs were sampled in the transects perpendicular to the shoreline, at the river inflow and the frontal dam. The total concentration of Mn, Zn, Pb, Cd, Cu, Cr and Ni was determined by ICP-EAS method after the sample digestion in the mixture of concentrated HNO3 and HClO4 acids. The statistical analyses: value intervals, mean values, variation coefficient, the median and the skewed distribution were performed. To estimate differences between the means for transects, Tukey’s test was applied with least significant difference (LSD) determination. The maps of the metal spatial distribution were drawn and sediment quality according to the geochemical and ecotoxicological criteria evaluated. Differences between the reservoirs in terms of heavy metals concentration in bottom sediments, and regularities in their spatial distribution were found. In the ZZ sediments the concentration was at the level of geochemical background (Zn, Cr), slightly (Cd, Cu, Ni) or moderately (Pb) contaminated sediments. The metal concentration in the sediments of the BI was up to eight times higher as compared to the ZZ. Moreover, sediments from the BI reservoir showed a greater variability of metal concentration than those from ZZ, which resulted from the dredging operation performed in the part of the reservoir. Metal concentration in sediments of the dredged part was ca. 2–5 times lower than in the undredged one, which indicates that after the dredging operation, accumulation of these metals was slight. The concentrations of Zn, Pb and Cd from the undredged part of BI were at the level of contaminated sediments and exceeded the probable effects level (PEL). In the ZZ, the greatest accumulation of metals occurred in the upper part of the reservoir and at the frontal dam, and the lowest in the middle part of the reservoir. In BI, the lower outflow of water in this reservoir caused a lower metal concentration in the sediments at the frontal dam, as compared with the other sediments in the undredged part of the reservoir. The results indicate that in small and shallow reservoirs, areas of accumulation of heavy metals depend on such factors as a parent river current, reservoir depth, water waving, reservoir shape (narrowing, coves/bays), and type of water outflow.
The assessment of drinking water quality using zero unitarization method
Authors: Radzka Elżbieta , Rymuza Katarzyna , Jankowska Jolanta
Published: November 2015

The work is an attempt to assess piped water quality in four counties located in east central Poland. Piped water was analysed for three successive years in each county. Water samples were tested for the following physical and chemical parameters: turbidity, colour, conductivity, taste, odour, pH, nitrates (III), nitrates (V), iron and manganese. They were compared with the current standard values. Preliminary data analysis included an analysis of maximum and minimum values of physical and chemical parameters, and it revealed that turbidity, colour, iron and manganese contents exceeded the permissible standards in all the counties. Percentages of parameters exceedances and mean values of the exceedances were used to rank the counties in terms of water quality. The ranking was obtained by means of multidimensional comparative analysis. It was demonstrated that best quality water was supplied by Węgrów County water supply system which was followed by Mińsk Mazowiecki County. The third rank was assigned to Łosice County and the poorest quality water was found to be supplied by Siedlce County water supply system.
Cerivastatin represses atherogenic gene expression through the induction of KLF2 via isoprenoid metabolic pathways
Authors: Zhao Jiyuan , Natarajan Selvamuthu K. , Chronos Nicolas , Singh Jai Pal
Published: November 2015

Earlier clinical studies have reported that cerivastatin has an antiatherosclerotic effect that is unique among the statins. In our study, human THP-1 macrophage cells were used to study the effects of various statins on the expressions of the atherosclerotic genes and Kruppel-like factor 2 (KLF2). Cerivastatin significantly inhibited the two atherosclerotic genes, monocyte chemoattractant protein-1 (MCP-1) and C-C chemokine receptor type 2 (CCR2) at both the mRNA and protein levels, while the other statins did not. Accordingly, cerivastatin was also the most potent inducer of KLF2 transcription in the macrophages. An siRNA-induced reduction in KLF2 expression blocked the inhibition of MCP-1 and CCR2 by cerivastatin. When the cells were further treated with mevalonate, farnesylpyrophosphate (FPP) or geranylgeranyl pyrophosphate (GGPP), the effects of cerivastatin on KLF2, MCP-1 and CCR2 were obviously reversed. Thus, the results showed that cerivastatin was a potent inhibitor of the inflammation genes MCP-1 and CCR2 through the induction of KLF2. The regulation of MCP-1, CCR2 and KLF2 by cerivastatin was isoprenoid pathway dependent. Our studies suggest that the effect of cerivastatin on atherosclerotic genes and KLF2 expression may contribute to the cardioprotection observed in reported clinical studies.
Geological interpretation of magnetotelluric sounding in the southern part of seismic profile 2T (Central Slovakia)
Authors: Bezák Vladimír , Pek Josef , Majcin Dušan , Bučová Jana , Šoltis Tomáš , Bilčík Dušan , Klanica Radek
Published: November 2015

In this paper we present a geological interpretation of magnetotelluric sounding along the southern part of the seismic 2T profile situated in the southern Central Slovakia. The complexes with higher conductivity are imaged in the shallow depths, formed by the Tertiary sediments and volcanics. In the northernmost part of the profile, the influence of non-conductive complexes composed of orthogneisses and overlying Mesozoic carbonates is significant. In the central part of the profile, the low conductive granitoid complexes are superposed over the metamorphic rocks with higher conductivity. This structure is a remnant of the Hercynian middle crust nappes. The most outstanding phenomenon of the profile is the sudden, almost step change in the conductivity parameters of the crust in the southern part. The significantly high conductivity of the crust in this area is most probably not related to its lithological composition, but by the abundant supply of fluids in the crust connected with the Neogene tectonic and volcanic processes.
Perennial Philology and the Ideal of the White Overall
Authors: Bernardes José Augusto Cardoso
Published: November 2015

Joining the university context in the middle of the 19th century, Philology served as a comprehensive basis for what nowadays is meant by literary and linguistic studies. Depending on the specialization tendency that would settle down in the academic context (with regard to either the formative offer or the foundation of various research fields), each of these areas followed separate or even divergent paths, losing, to a great extent, the contact with its initial basis. Despite this state of affairs, Philology has displayed a strong capacity of resistance, maintaining its traditional dimension active or going through metamorphoses that resulted from the incorporation of new technologies, as well as from the epistemological adjustment that enabled it to overcome its first positivist stages. Trying to find a new place inside the general framework of Social Sciences and Humanities, literary studies need to recover its order and credibility, two factors that the new face of Philology can inspire. The present study aims at reconstructing the most recent trajectory undergone by this field of research and education, by identifying a space of reconnection that already seems to be adequate and beneficial.
Unveiling the Individual Memory of War in the Work of Maïssa Bey
Authors: Yılancıoglu S. Seza
Published: November 2015

This paper is interested in the individual memory of wars in Maïssa Bey. The writer devoted her two books to the wars in Algeria - they were written to be adapted to the theatre: Entendez-vous dans les montagnes… (2002) and Pierre Sang Papier ou Cendre (2008). In Entendez-vous dans les montagnes..., the memory in question is that of the War of Independence against the colonization during the years 1956-1962, while Pierre Sang Papier ou Cendre addresses the French colonization that lasted 132 years, from 1830 to 1962. In other words, the first relies on individual and collective memories, while the second concerns especially the collective memory.
Vintilă Horia and Trans-Temporal Travel
Authors: Crăciunescu Pompiliu
Published: November 2015

The Romanian-born European writer Vintilă Horia - whose birth centenary is celebrated this year - was a genuine searcher of truth. His entire work pleads for transgressive-integrating knowledge, in opposition to binary logic and scientism; it is the privileged space of articulation between cognition, creation and gnosis, between the apophatism of science, mystic apofatism and artistic apofatism. Although much less known than the trilogy of exile - Dieu est né en exil (1960), Le chevalier de la résignation (1961) and ¡Perseguid a Boecio! (1983) - the small-sized novel Le voyage à San Marcos (1972) acts as an exemplary attestation to this pompous conjunction. The current article focuses especially on the text’s trans-temporal valence
Tubo-ovarian abscess in non sexually active adolescents
Authors: Alsahabi Jawaher A. , Aldakhil Lateefa O. , Alobaid Abdulaziz S.
Published: November 2015

A tubo-ovarian abscess is a rare presentation in non-sexually active adolescents; only 11 cases have been reported in the literature. Variable approaches for diagnosis and management are described. We present a 19-year-old, non-sexually active, medically free girl, who had an abdominopelvic mass with abdominal pain and vomiting followed by fever. She had a confusing presentation of malignancy versus tuberculosis, with the help of imaging, diagnosis and treatment with percutaneous drainage, conservative treatment was achieved. Diagnosis of a tubo-ovarian abscess is difficult in non-sexually active adolescents, a high clinical index of suspicion is important as misdiagnosis may lead to radical and aggressive management, conservative management is possible in many of these patients.
Prevalence and correlates of suicidal ideation and attempts among children and adolescents
Authors: Sampasa-Kanyinga Hugues , Dupuis Lorette C. , Ray Robin
Published: November 2015

Suicide is a potentially preventable public health issue. It is therefore important to examine its immediate precursors, including suicidal ideation and attempts, to help in the development of future public health interventions. The present study reports the prevalence of suicidal ideation and attempts in the past 12 months in children and adolescents and identifies correlates of such behaviors in a large and diverse sample of middle and high school students. Data were drawn from a representative sample of Ottawa students (n=1922) aged 11–20 years (14.4±1.9 years) from three cycles (2009, 2011 and 2013) of the Ontario Student Drug Use and Health Survey (OSDUHS), a cross-sectional school-based appraisal of students in grades 7–12 across Ontario, Canada. Overall, 10.8% of students exhibited suicidal ideation and 3.0% reported suicide attempts in the past 12 months. The conditional probability of making an attempt was 25.5% among suicide ideators. Multivariable analyses indicated that being a girl and using alcohol and cannabis were positively associated with suicidal ideation, while tobacco was positively associated with suicide attempts. Being a victim of school bullying was significantly associated with reports of suicidal ideation and attempts, whereas school connectedness had protective effects against both suicidal ideation and attempts. These results indicate that suicidal ideation and attempts are related to other risky behaviors. Suicide-prevention efforts should be integrated within broader health-promoting initiatives.
Characteristics of the most viewed YouTube™ videos related to bullying
Authors: Basch Corey H. , Ruggles Kelly V. , Berdnik Alyssa , Basch Charles E.
Published: November 2015

Bullying is an intentional act that can wreak havoc in the life of an individual. With more than 1 billion users, YouTube™ is a powerful medium for disseminating information. The purpose of this study was to describe the extent to which content related to bullying is present on YouTube™ with respect to source, content, number of views, length, and year uploaded. Collectively, the videos in this sample were viewed more than half a billion times. The source of the most widely viewed videos was consumers, and none of the most widely viewed videos was posted by a governmental agency or a professional organization. The most common content in the videos was describing or depicting violence (n=89). Over one-half addressed getting help (n=56). Suicide was mentioned in 38 of the videos. Additional investment by professional agencies is warranted to improve understanding about ways to increase the dissemination of positive messages about bullying prevention, and about helping adolescents who are bullied on social media.
Invasive Candida Infections in the ICU: Diagnosis and Therapy
Authors: Hankovszky Péter , Társy Domokos , Öveges Nándor , Molnár Zsolt
Published: November 2015

Invasive fungal infections have become a serious problem in the critically ill. One of the main reasons is the development of an immunocompromised condition. The most frequently found pathogens are Candida species. In order to provide adequate treatment, understanding this potentially life-threatening infection is mandatory. The aim of this summary is to view Candida infections from a different perspective and to give an overview on epidemiology, the range of pathophysiology from colonization to the invasive infections, and its impact on mortality. New therapeutic options will also be discussed and how these relate to current guidelines. Finally, the key issue of the choice of antifungal agents will be evaluated.
Sudden Cardiac Death and Post Cardiac Arrest Syndrome. An Overview
Authors: Zima Endre
Published: November 2015

A satisfactory neurologic outcome is the key factor for survival in patients with sudden cardiac death (SCD), however this is highly dependent on the haemodynamic status. Short term cardiopulmonary resuscitation and regained consciousness on the return of spontaneous circulation (ROSC) is indicative of a better prognosis. The evaluation and treatment of SCD triggering factors and of underlying acute and chronic diseases will facilitate prevention and lower the risk of cardiac arrest. Long term CPR and a prolonged unconscious status after ROSC, in the Intensive Care Units or Coronary Care Units, indicates the need for specific treatment and supportive therapy including efforts to prevent hyperthermia. The prognosis of these patients is unpredictable within the first seventy two hours, due to unknown responses to therapeutic management and the lack of specific prognostic factors. Patients in these circumstances require the highest level of intensive care and aetiology driven treatment without any delay, independently of their coma state. Current guidelines sugest the use of multiple procedures in arriving at a diagnosis and prognosis of these critical cases.
30 years of General Statistical Analysis and canonical equation K
60 for Hermitian matrices
(A + B
U
C)(A + B
U
C)*, where U is a random unitary matrix
Authors: Girko Vyacheslav L.
Published: November 2015

In this paper we apply the REFORM method for the
deduction of the system of canonical equations K
60 for normalized spectral functions of
the matrices [An
+ Bn

Un
(ε)Cn
][An
+ Bn

Un
(ε)Cn
]*.
Colaboración Universidad-Escuela para el cambio escolar. Una investigación-acción en proceso
Authors: Álvarez Álvarez Carmen , Osoro Sierra José Manuel
Published: November 2015

Son infrecuentes las relaciones de colaboración entre las universidades españolas y las escuelas para favorecer el desarrollo profesional docente, pese a lo importantes que podrían ser éstas. Con frecuencia la universidad está escorada hacia la investigación y la escuela hacia la enseñanza, de tal manera que sólo se producen intercambios entre estas instituciones cuando una precisa de la otra. En estos casos puede hablarse de relaciones instrumentales Universidad-Escuela. Sólo cuando se produce un intercambio interinstitucional para favorecer el desarrollo profesional de académicos y prácticos podría hablarse de verdadera relación Universidad-Escuela. En este caso podría hablarse de relaciones de colaboración. En el grueso del artículo se expone cómo se ha desarrollado un proceso de colaboración entre nuestra universidad y un centro público de Educación Infantil y Primaria para favorecer la superación de algunas dificultades escolares. Tras un proceso de análisis de necesidades se estimó que lo más conveniente para el centro era tratar de implementar algunas estrategias didácticas novedosas (grupos interactivos y tertulias literarias). El proceso innovador desarrollado ha permitido iniciar, desarrollar e institucionalizar el cambio escolar, favoreciéndose el desarrollo profesional de académicos y prácticos y la mejora de la relaciones Universidad-Escuela.http://dx.doi.org/10.15304/ie.24.1483
El aprendizaje cooperativo en un centro de primaria: una experiencia inclusiva
Authors: Pedreira Villar Marina , González Fontao María Pilar
Published: November 2015

En este artículo se describe una experiencia inclusiva de un alumno con Trastorno Generalizado del Desarrollo (TXD) en un centro de primaria a través de la metodología del aprendizaje cooperativo. La práctica se contextualiza en un grupo de alumnos/as del segundo ciclo de primaria. En diferentes textos se detalla el proceso de formación que se consolidó, la aplicación de la metodología cooperativa y las fases de desarrollo. La visión de la profesora tutora y de la profesora de apoyo encabezan esta práctica educativa. El éxito de la experiencia apunta al impacto que se obtiene al introducir metodologías que favorecen  la inclusión del alumnado en los centros educativos. Las conclusiones finales se centran no sólo en los resultados y mejoras obtenidas para el alumnado, sino en aquellas que se refieren al profesorado y al centro educativo.http://dx.doi.org/10.15304/ie.24.1671
The Founder Strains of the Collaborative Cross Express a Complex Combination of Advantageous and Deleterious Traits for Male Reproduction
Authors: Odet Fanny , Pan Wenqi , Bell Timothy A , Goodson Summer G , Stevans Alicia M , Yun Zianing , Aylor David L , Kao Chia-Yu , McMillan Leonard , de Villena Fernando Pardo-Manuel , O’Brien Deborah A
Published: November 2015

Surveys of inbred strains of mice are standard approaches to determine the heritability and range of phenotypic variation for biomedical traits. In addition, they may lead to the identification of novel phenotypes and models of human disease. Surprisingly, male reproductive phenotypes are among the least-represented traits in the Mouse Phenome Database. Here we report the results of a broad survey of the eight founder inbred strains of both the Collaborative Cross (CC) and the Diversity Outbred populations, two new mouse resources that are being used as platforms for systems genetics and sources of mouse models of human diseases. Our survey includes representatives of the three main subspecies of the house mice and a mix of classical and wild-derived inbred strains. In addition to standard staples of male reproductive phenotyping such as reproductive organ weights, sperm counts, and sperm morphology, our survey includes sperm motility and the first detailed survey of testis histology. As expected for such a broad survey, heritability varies widely among traits. We conclude that although all eight inbred strains are fertile, most display a mix of advantageous and deleterious male reproductive traits. The CAST/EiJ strain is an outlier, with an unusual combination of deleterious male reproductive traits including low sperm counts, high levels of morphologically abnormal sperm, and poor motility. In contrast, sperm from the PWK/PhJ and WSB/EiJ strains had the greatest percentages of normal morphology and vigorous motility. Finally, we report an abnormal testis phenotype that is highly heritable and restricted to the WSB/EiJ strain. This phenotype is characterized by the presence of a large, but variable, number of vacuoles in at least 10% of the seminiferous tubules. The onset of the phenotype between 2 and 3 wk of age is temporally correlated with the formation of the blood-testis barrier. We speculate that this phenotype may play a role in high rates of extinction in the CC project and in the phenotypes associated with speciation in genetic crosses that use the WSB/EiJ strain as representative of the Mus muculus domesticus subspecies.
Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing
Authors: Shoemaker Lorelei D , Clark Michael J , Patwardhan Anil , Chandratillake Gemma , Garcia Sarah , Chen Rong , Morgan Alexander A , Leng Nan , Kirk Scott , Chen Richard , Cook Douglas J , Snyder Michael , Steinberg Gary K
Published: November 2015

Moyamoya disease (MMD) is a rare disorder characterized by cerebrovascular occlusion and development of hemorrhage-prone collateral vessels. Approximately 10–12% of cases are familial, with a presumed low penetrance autosomal dominant pattern of inheritance. Diagnosis commonly occurs only after clinical presentation. The recent identification of the RNF213 founder mutation (p.R4810K) in the Asian population has made a significant contribution, but the etiology of this disease remains unclear. To further develop the variant landscape of MMD, we performed high-depth whole exome sequencing of 125 unrelated, predominantly nonfamilial, ethnically diverse MMD patients in parallel with 125 internally sequenced, matched controls using the same exome and analysis platform. Three subpopulations were established: Asian, Caucasian, and non-RNF213 founder mutation cases. We provided additional support for the previously observed RNF213 founder mutation (p.R4810K) in Asian cases (P = 6.01×10−5) that was enriched among East Asians compared to Southeast Asian and Pacific Islander cases (P = 9.52×10−4) and was absent in all Caucasian cases. The most enriched variant in Caucasian (P = 7.93×10−4) and non-RNF213 founder mutation (P = 1.51×10−3) cases was ZXDC (p.P562L), a gene involved in MHC Class II activation. Collapsing variant methodology ranked OBSCN, a gene involved in myofibrillogenesis, as most enriched in Caucasian (P = 1.07×10−4) and non-RNF213 founder mutation cases (P = 5.31×10−5). These findings further support the East Asian origins of the RNF213 (p.R4810K) variant and more fully describe the genetic landscape of multiethnic MMD, revealing novel, alternative candidate variants and genes that may be important in MMD etiology and diagnosis.
Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid Wheat
Authors: Edae Erena A , Bowden Robert L , Poland Jesse
Published: November 2015

The advancement of next-generation sequencing technologies in conjunction with new bioinformatics tools enabled fine-tuning of sequence-based, high-resolution mapping strategies for complex genomes. Although genotyping-by-sequencing (GBS) provides a large number of markers, its application for association mapping and genomics-assisted breeding is limited by a large proportion of missing data per marker. For species with a reference genomic sequence, markers can be ordered on the physical map. However, in the absence of reference marker order, the use and imputation of GBS markers is challenging. Here, we demonstrate how the population sequencing (POPSEQ) approach can be used to provide marker context for GBS in wheat. The utility of a POPSEQ-based genetic map as a reference map to create genetically ordered markers on a chromosome for hexaploid wheat was validated by constructing an independent de novo linkage map of GBS markers from a Synthetic W7984 × Opata M85 recombinant inbred line (SynOpRIL) population. The results indicated that there is strong agreement between the independent de novo linkage map and the POPSEQ mapping approach in mapping and ordering GBS markers for hexaploid wheat. After ordering, a large number of GBS markers were imputed, thus providing a high-quality reference map that can be used for QTL mapping for different traits. The POPSEQ-based reference map and whole-genome sequence assemblies are valuable resources that can be used to order GBS markers and enable the application of highly accurate imputation methods to leverage the application GBS markers in wheat.
Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments
Authors: Kumar Satish , Molloy Claire , Muñoz Patricio , Daetwyler Hans , Chagné David , Volz Richard
Published: November 2015

The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families.
Developmental Function of the PHR Protein RPM-1 Is Required for Learning inCaenorhabditis elegans
Authors: Giles Andrew C , Opperman Karla J , Rankin Catharine H , Grill Brock
Published: November 2015

The PAM/Highwire/RPM-1 (PHR) proteins are signaling hubs that function as important regulators of neural development. Loss of function in Caenorhabditis elegans rpm-1 and Drosophila Highwire results in failed axon termination, inappropriate axon targeting, and abnormal synapse formation. Despite broad expression in the nervous system and relatively dramatic defects in synapse formation and axon development, very mild abnormalities in behavior have been found in animals lacking PHR protein function. Therefore, we hypothesized that large defects in behavior might only be detected in scenarios in which evoked, prolonged circuit function is required, or in which behavioral plasticity occurs. Using quantitative approaches in C. elegans, we found that rpm-1 loss-of-function mutants have relatively mild abnormalities in exploratory locomotion, but have large defects in evoked responses to harsh touch and learning associated with tap habituation. We explored the nature of the severe habituation defects in rpm-1 mutants further. To address what part of the habituation circuit was impaired in rpm-1 mutants, we performed rescue analysis with promoters for different neurons. Our findings indicate that RPM-1 function in the mechanosensory neurons affects habituation. Transgenic expression of RPM-1 in adult animals failed to rescue habituation defects, consistent with developmental defects in rpm-1 mutants resulting in impaired habituation. Genetic analysis showed that other regulators of neuronal development that function in the rpm-1 pathway (including glo-4, fsn-1, and dlk-1) also affected habituation. Overall, our findings suggest that developmental defects in rpm-1 mutants manifest most prominently in behaviors that require protracted or plastic circuit function, such as learning.
Heterosis Increases Fertility, Fecundity, and Survival of Laboratory-Produced F1 Hybrid Males of the Malaria Mosquito Anopheles coluzzii
Authors: Ekechukwu Nkiru E , Baeshen Rowida , Traorè Sékou F , Coulibaly Mamadou , Diabate Abdoulaye , Catteruccia Flaminia , Tripet Frédéric
Published: November 2015

The success of vector control strategies aiming to decrease disease transmission via the release of sterile or genetically-modified male mosquitoes critically depends on mating between laboratory-reared males and wild females. Unfortunately, mosquito colonization, laboratory rearing, and genetic manipulations can all negatively affect male competitiveness. Heterosis is commonly used to produce domestic animals with enhanced vigor and homogenous genetic background and could therefore potentially improve the mating performance of mass-reared male mosquitoes. Here, we produced enhanced hybrid males of the malaria mosquito Anopheles coluzzii by crossing two strains colonized >35 and 8 years ago. We compared the amount of sperm and mating plug proteins they transferred to females, as well as their insemination rate, reproductive success and longevity under various experimental conditions. Across experiments, widespread adaptations to laboratory mating were detected in the older strain. In large-group mating experiments, no overall hybrid advantage in insemination rates and the amount of sperm and accessory gland proteins transferred to females was detected. Despite higher sperm activity, hybrid males did not appear more fecund. However, individual-male mating and laboratory-swarm experiments revealed that hybrid males, while inseminating fewer females than older inbred males, were significantly more fertile, producing larger mating plugs and drastically increasing female fecundity. Heterotic males also showed increased longevity. These results validate the use of heterosis for creating hybrid males with improved fitness from long-established inbred laboratory strains. Therefore, this simple approach could facilitate disease control strategies based on male mosquito releases with important ultimate benefits to human health.
Turnover of Sex Chromosomes in Celebensis Group Medaka Fishes
Authors: Myosho Taijun , Takehana Yusuke , Hamaguchi Satoshi , Sakaizumi Mitsuru
Published: November 2015

Sex chromosomes and the sex-determining (SD) gene are variable in vertebrates. In particular, medaka fishes in the genus Oryzias show an extremely large diversity in sex chromosomes and the SD gene, providing a good model to study the evolutionary process by which they turnover. Here, we investigated the sex determination system and sex chromosomes in six celebensis group species. Our sex-linkage analysis demonstrated that all species had an XX-XY sex determination system, and that the Oryzias marmoratus and O. profundicola sex chromosomes were homologous to O. latipes linkage group (LG) 10, while those of the other four species, O. celebensis, O. matanensis, O. wolasi, and O. woworae, were homologous to O. latipes LG 24. The phylogenetic relationship suggested a turnover of the sex chromosomes from O. latipes LG 24 to LG 10 within this group. Six sex-linkage maps showed that the former two and the latter four species shared a common SD locus, respectively, suggesting that the LG 24 acquired the SD function in a common ancestor of the celebensis group, and that the LG 10 SD function appeared in a common ancestor of O. marmoratus and O. profundicola after the divergence of O. matanensis. Additionally, fine mapping and association analysis in the former two species revealed that Sox3 on the Y chromosome is a prime candidate for the SD gene, and that the Y-specific 430-bp insertion might be involved in its SD function.
Examination of Endogenous Rotund Expression and Function in DevelopingDrosophilaOlfactory System Using CRISPR-Cas9–Mediated Protein Tagging
Authors: Li Qingyun , Barish Scott , Okuwa Sumie , Volkan Pelin C
Published: November 2015

The zinc-finger protein Rotund (Rn) plays a critical role in controlling the development of the fly olfactory system. However, little is known about its molecular function in vivo. Here, we added protein tags to the rn locus using CRISPR-Cas9 technology in Drosophila to investigate its subcellular localization and the genes that it regulates . We previously used a reporter construct to show that rn is expressed in a subset of olfactory receptor neuron (ORN) precursors and it is required for the diversification of ORN fates. Here, we show that tagged endogenous Rn protein is functional based on the analysis of ORN phenotypes. Using this method, we also mapped the expression pattern of the endogenous isoform-specific tags in vivo with increased precision. Comparison of the Rn expression pattern from this study with previously published results using GAL4 reporters showed that Rn is mainly present in early steps in antennal disc patterning, but not in pupal stages when ORNs are born. Finally, using chromatin immunoprecipitation, we showed a direct binding of Rotund to a previously identified regulatory element upstream of the bric-a-brac gene locus in the developing antennal disc.
Dynamics ofWolbachia pipientisGene Expression Across theDrosophila melanogasterLife Cycle
Authors: Gutzwiller Florence , Carmo Catarina R , Miller Danny E , Rice Danny W , Newton Irene L G , Hawley R Scott , Teixeira Luis , Bergman Casey M
Published: November 2015

Symbiotic interactions between microbes and their multicellular hosts have manifold biological consequences. To better understand how bacteria maintain symbiotic associations with animal hosts, we analyzed genome-wide gene expression for the endosymbiotic α-proteobacteria Wolbachia pipientis across the entire life cycle of Drosophila melanogaster. We found that the majority of Wolbachia genes are expressed stably across the D. melanogaster life cycle, but that 7.8% of Wolbachia genes exhibit robust stage- or sex-specific expression differences when studied in the whole-organism context. Differentially-expressed Wolbachia genes are typically up-regulated after Drosophila embryogenesis and include many bacterial membrane, secretion system, and ankyrin repeat-containing proteins. Sex-biased genes are often organized as small operons of uncharacterized genes and are mainly up-regulated in adult Drosophila males in an age-dependent manner. We also systematically investigated expression levels of previously-reported candidate genes thought to be involved in host-microbe interaction, including those in the WO-A and WO-B prophages and in the Octomom region, which has been implicated in regulating bacterial titer and pathogenicity. Our work provides comprehensive insight into the developmental dynamics of gene expression for a widespread endosymbiont in its natural host context, and shows that public gene expression data harbor rich resources to probe the functional basis of the Wolbachia-Drosophila symbiosis and annotate the transcriptional outputs of the Wolbachia genome.
Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean
Authors: Song Xiaofeng , Wei Haichao , Cheng Wen , Yang Suxin , Zhao Yanxiu , Li Xuan , Luo Da , Zhang Hui , Feng Xianzhong
Published: November 2015

Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5–50 bp in length were chosen for validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean.
SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing
Authors: Guo Xiaoge , Lehner Kevin , O’Connell Karen , Zhang Jenny , Dave Sandeep S , Jinks-Robertson Sue
Published: November 2015

Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses.
A Major Locus Controls a Genital Shape Difference Involved in Reproductive Isolation BetweenDrosophila yakubaandDrosophila santomea
Authors: Peluffo Alexandre E , Nuez Isabelle , Debat Vincent , Savisaar Rosina , Stern David L , Orgogozo Virginie
Published: November 2015

Rapid evolution of genitalia shape, a widespread phenomenon in animals with internal fertilization, offers the opportunity to dissect the genetic architecture of morphological evolution linked to sexual selection and speciation. Most quantitative trait loci (QTL) mapping studies of genitalia divergence have focused on Drosophila melanogaster and its three most closely related species, D. simulans, D. mauritiana, and D. sechellia, and have suggested that the genetic basis of genitalia evolution involves many loci. We report the first genetic study of male genitalia evolution between D. yakuba and D. santomea, two species of the D. melanogaster species subgroup. We focus on male ventral branches, which harm females during interspecific copulation. Using landmark-based geometric morphometrics, we characterized shape variation in parental species, F1 hybrids, and backcross progeny and show that the main axis of shape variation within the backcross population matches the interspecific variation between parental species. For genotyping, we developed a new molecular method to perform multiplexed shotgun genotyping (MSG), which allowed us to prepare genomic DNA libraries from 365 backcross individuals in a few days using little DNA. We detected only three QTL, one of which spans 2.7 Mb and exhibits a highly significant effect on shape variation that can be linked to the harmfulness of the ventral branches. We conclude that the genetic architecture of genitalia morphology divergence may not always be as complex as suggested by previous studies.
Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing
Authors: Guo Jianjun , Fan Jue , Hauser Bernard A , Rhee Seung Y
Published: November 2015

Complex traits such as crop performance and human diseases are controlled by multiple genetic loci, many of which have small effects and often go undetected by traditional quantitative trait locus (QTL) mapping. Recently, bulked segregant analysis with large F2 pools and genome-level markers (named extreme-QTL or X-QTL mapping) has been used to identify many QTL. To estimate parameters impacting QTL detection for X-QTL mapping, we simulated the effects of population size, marker density, and sequencing depth of markers on QTL detectability for traits with differing heritabilities. These simulations indicate that a high (>90%) chance of detecting QTL with at least 5% effect requires 5000× sequencing depth for a trait with heritability of 0.4−0.7. For most eukaryotic organisms, whole-genome sequencing at this depth is not economically feasible. Therefore, we tested and confirmed the feasibility of applying deep sequencing of target-enriched markers for X-QTL mapping. We used two traits in Arabidopsis thaliana with different heritabilities: seed size (H2 = 0.61) and seedling greening in response to salt (H2 = 0.94). We used a modified G test to identify QTL regions and developed a model-based statistical framework to resolve individual peaks by incorporating recombination rates. Multiple QTL were identified for both traits, including previously undiscovered QTL. We call our method target-enriched X-QTL (TEX-QTL) mapping; this mapping approach is not limited by the genome size or the availability of recombinant inbred populations and should be applicable to many organisms and traits.