bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing linkage and association analyses in sheep points to a better way of doing GWAS
Authors: KEMPER KATHRYN E. , DAETWYLER HANS D. , VISSCHER PETER M. , GODDARD MICHAEL E. 
Published: September 2012

SummaryGenome wide association studies (GWAS) have largely succeeded family-based linkage studies in livestock and human populations as the preferred method to map loci for complex or quantitative traits. However, the type of results produced by the two analyses contrast sharply due to differences in linkage disequilibrium (LD) imposed by the design of studies. In this paper, we demonstrate that association and linkage studies are in agreement provided that (i) the effects from both studies are estimated appropriately as random effects, (ii) all markers are fitted simultaneously and (iii) appropriate adjustments are made for the differences in LD between the study designs. We demonstrate with real data that linkage results can be predicted by the sum of association effects. Our association study captured most of the linkage information because we could predict the linkage results with moderate accuracy. We suggest that the ability of common single nucleotide polymorphism (SNP) to capture the genetic variance in a population will depend on the effective population size of the study organism. The results provide further evidence for many loci of small effect underlying complex traits. The analysis suggests a more informed method for GWAS is to fit statistical models where all SNPs are analysed simultaneously and as random effects.
Sequence variations inOsAGPasesignificantly associated with amylose content and viscosity properties in rice (Oryza sativaL.)
Authors: LU FU-HAO , PARK YONG-JIN 
Published: September 2012

SummarySequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativaL.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. AnADP-glucose pyrophosphorylase small unit 1(OsAGPS1) SNP (A–G) was significantly associated with increased AC (P<0·001,R2=15·6%), while a 12-bp deletion ofAGPase large unit 4(OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0·001,R2=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.
Polish stress: looking for phonetic evidence of a bidirectional system
Authors: Newlin-Łukowicz Luiza 
Published: September 2012

AbstractThis paper reports on a study of Polish stress, the only uncontested example of a bidirectional system with internal lapses (Kager 2001, McCarthy 2003). The results indicate that Polish stress is non-iterative, a finding that seriously calls into question the existence of this particular stress type. An analysis of the acoustic prominence of syllables traditionally associated with different stress levels suggests that Polish simple words exhibit only one (penultimate) prominence. The stress pattern in compounds is less uniform; they can carry one or two (penultimate) stresses, depending on their prosodic structure. I analyse the distribution of stresses in compounds as governed by clash avoidance. Specifically, compound stems are parsed into separate PWds and assigned separate stresses only if the emergent trochees are non-adjacent. Hence, four-syllable compounds like /tsuʤɔ-ˈʑεmʲεts/ ‘foreigner’ have one stress, while compounds like /banaˈnɔvɔ-arbuˈzɔvɨ/ ‘banana-watermelon’ have two. I ascribe this pattern to the undominated ranking of the *FtFtconstraint.
Genetic Factors Account for Half of the Phenotypic Variance in Liability to Sleep-Related Bruxism in Young Adults: A Nationwide Finnish Twin Cohort Study
Authors: Rintakoski Katariina , Hublin Christer , Lobbezoo Frank , Rose Richard J. , Kaprio Jaakko 
Published: September 2012

Objectives: The aim of the present study was to examine the role of genetic and environmental factors in the phenotypic variance of bruxism in a large population-based cohort of young adult twins in Finland.Methods: The material of the present study derives from the FinnTwin16 cohort study consisting of five birth cohorts of twin pairs born in 1975–1979 who completed a questionnaire (at mean age 24, range 23–27 years) with data on frequency of sleep-related bruxism in 2000–2002. We used quantitative genetic modeling, based on the genetic similarity of monozygotic and dizygotic twins, to estimate the most probable genetic model for bruxism, based on decomposition of phenotypic variance into components: additive genetic effects (A), dominant genetic effects (D), and non-shared environmental effects (E).Results: On average, 8.7% experienced bruxism weekly, 23.4% rarely, and 67.9% never, with no significant gender difference (p = .052). The best fitting genetic model for bruxism was the AE-model. Additive genetic effects accounted for 52% (95% CI 0.41–0.62) of the total phenotypic variance. Sex-limitation model revealed no gender differences.Conclusions: Genetic factors account for a substantial proportion of the phenotypic variation of the liability to sleep-related bruxism, with no gender difference in its genetic architecture.
Auto‐acoustic compaction in steady shear flows: Experimental evidence for suppression of shear dilatancy by internal acoustic vibration
Authors: van der Elst Nicholas J. , Brodsky Emily E. , Le Bas Pierre‐Yves , Johnson Paul A. 
Published: September 2012

Granular shear flows are intrinsic to many geophysical processes, ranging from landslides and debris flows to earthquake rupture on gouge‐filled faults. The rheology of a granular flow depends strongly on the boundary conditions and shear rate. Earthquake rupture involves a transition from quasi‐static to rapid shear rates. Understanding the processes controlling the transitional rheology is potentially crucial for understanding the rupture process and the coseismic strength of faults. Here we explore the transition experimentally using a commercial torsional rheometer. We measure the thickness of a steady shear flow at velocities between 10−3 and 102 cm/s, at very low normal stress (7 kPa), and observe that thickness is reduced at intermediate velocities (0.1–10 cm/s) for angular particles, but not for smooth glass beads. The maximum reduction in thickness is on the order of 10% of the active shear zone thickness, and scales with the amplitude of shear‐generated acoustic vibration. By examining the response to externally applied vibration, we show that the thinning reflects a feedback between internally generated acoustic vibration and granular rheology. We link this phenomenon to acoustic compaction of a dilated granular medium, and formulate an empirical model for the steady state thickness of a shear‐zone in which shear‐induced dilatation is balanced by a newly identified mechanism we call auto‐acoustic compaction. This mechanism is activated when the acoustic pressure is on the order of the confining pressure, and results in a velocity‐weakening granular flow regime at shear rates four orders of magnitude below those previously associated with the transition out of quasi‐static granular flow. Although the micromechanics of granular deformation may change with greater normal stress, auto‐acoustic compaction should influence the rheology of angular fault gouge at higher stresses, as long as the gouge has nonzero porosity during shear.
The role of frictional strength on plate coupling at the subduction interface
Authors: Tan Eh , Lavier Luc L. , Van Avendonk Harm J. A. , Heuret Arnauld 
Published: September 2012

At a subduction zone the amount of friction between the incoming plate and the forearc is an important factor in controlling the dip angle of subduction and the structure of the forearc. In this paper, we investigate the role of the frictional strength of sediments and of the serpentinized peridotite on the evolution of convergent margins. In numerical models, we vary thickness of a serpentinized layer in the mantle wedge (15 to 25 km) and the frictional strength of both the sediments and serpentinized mantle (friction angle 1° to 15°, or static friction coefficient 0.017 to 0.27) to control the amount of frictional coupling between the plates. With plastic strain weakening in the lithosphere, our numerical models can attain stable subduction geometry over millions of years. We find that the frictional strength of the sediments and serpentinized peridotite exerts the largest control on the dip angle of the subduction interface at seismogenic depths. In the case of low sediment and serpentinite friction, the subduction interface has a shallow dip, while the subduction zone develops an accretionary prism, a broad forearc high, a deep forearc basin, and a shallow trench. In the high friction case, the subduction interface is steep, the trench is deeper, and the accretionary prism, forearc high and basin are all absent. The resultant free‐air gravity and topographic signature of these subduction zone models are consistent with observations. We believe that the low‐friction model produces a geometry and forearc structure similar to that of accretionary margins. Conversely, models with high friction angles in sediments and serpentinite develop characteristics of an erosional convergent margin. We find that the strength of the subduction interface is critical in controlling the amount of coupling at the seismogenic zone and perhaps ultimately the size of the largest earthquakes at subduction zones.
Long‐term, non‐local coastline responses to local shoreline stabilization
Authors: Ells Kenneth , Murray A. Brad 
Published: September 2012

The future of large‐scale coastline evolution will be strongly coupled to human manipulations designed to prevent erosion. We explore the consequences of this coupling using a numerical model for large‐scale coastline evolution to compare the long‐term, non‐local effects of two generalized classes of shoreline stabilization: 1) beach nourishment (the addition of dredged sand to an eroding beach), and 2) hard‐structures (e.g., seawalls, groynes, etc.) which fix the position of the shoreline without adding sand. In centurial model experiments where localized stabilization is maintained in the context of changing climate forcing, both forms of stabilization are found to significantly alter patterns of erosion and accretion at distances up to tens of kilometers. On a cuspate‐cape coastline similar to the North and South Carolina coast, USA, with stabilization applied to the eroding updrift flank of a single cape, perturbations to coastline evolution are qualitatively similar within ∼20 km for each stabilization scenario, though they differ in magnitude both updrift and downdrift of the stabilized shoreline. The “human” signal in coastline change can extend as far as a neighboring cape (approximately 100 km away), but these long‐range effects differ for each scenario. Nourishment resulted in seaward growth of the stabilized cape, increasing the extent that it blocked sediment flux in downdrift regions of the coast through wave shadowing. When stabilized with a hard structure the cape's initial position remain fixed, decreasing wave shadowing.
The concept of wave‐turbopause layer and its signature in the global mesosphere‐lower thermospheric gravity wave activity
Authors: John Sherine Rachel , Kishore Kumar Karanam 
Published: September 2012

The concept of the ‘wave‐turbopause layer’ is introduced and discussed in this study, which defines the wave‐turbopause as a layer having a lower and upper boundary, where maximum dissipation of atmospheric waves happens. The analysis is carried out using three years of SABER temperature measurements (2004–2006) and seasonal and latitudinal variability of the wave‐turbopause layer is established. On an average, it is found that there is a maximum of ∼5–20 km difference in altitude between the lower and upper boundaries of the wave‐turbopause. Seasonally, the winter hemispheric high latitudes have the highest wave‐turbopause which decreases toward the summer hemisphere with a secondary maximum at the summer hemisphere midlatitude. Moreover, the monthly variability of the wave‐turbopause and mesopause is studied for 50°N, 0° and 50°S latitudes. On global scale, the latitude‐height sections of zonal mean gravity wave potential energy of the MLT region is compared with the wave‐turbopause characteristics. The wave‐turbopause pattern seems to be superposed on the potential energy transition pattern which exposes an intermediate layer sandwiched between low and high magnitudes of potential energy. Thus the present study proposes the concept of the wave‐turbopause layer and substantiates the same by discussing its latitudinal structure, seasonal and monthly variability, correlation with the cold point mesopause and gravity wave potential energy in the MLT region.
Introduction to Suomi national polar‐orbiting partnership advanced technology microwave sounder for numerical weather prediction and tropical cyclone applications
Authors: Weng F. , Zou X. , Wang X. , Yang S. , Goldberg M. D. 
Published: September 2012

The Suomi National Polar‐orbiting Partnership (NPP) satellite was successfully launched on 28 October 2011. On board the Suomi NPP, the Advanced Technology Microwave Sounder (ATMS) is a cross‐track scanning instrument and has 22 channels at frequencies ranging from 23 to 183 GHz which allows for probing the atmospheric temperature and moisture under clear and cloudy conditions. ATMS inherited most of the sounding channels from its predecessors: Advanced Microwave Sounding Unit‐A (AMSU‐A) and Microwave Humidity Sounder (MHS) onboard NOAA and MetOp satellites. However, ATMS has a wider scan swath and has no gaps between two consecutive orbits. It includes one new temperature sounding channel and two water vapor sounding channels and provides more details of thermal structures in lower troposphere, especially for the storm conditions such as tropical cyclones. While ATMS temperature sounding channels have shorter integration time and therefore higher noise than AMSU‐A, the ATMS observations from their overlapping field of views are resampled to produce AMSU‐A‐like measurements.
Upregulation of iHsp70 by mild heat shock protects rabbit myogenic stem cells: involvement of JNK signalling and c‐Jun
Authors: Bironaite Daiva , Pivoriunas Augustas , Venalis Algirdas 
Published: September 2012

AbstractiHsp70 [inducible Hsp70 (heat‐shock protein 70)] family members (iHsp70, Hsp72 and Hsp70) are highly conserved proteins that act as molecular chaperones and promote cell survival during various forms of stress. Our data indicate that cultured adult rabbit myoblasts do not express iHsp70 under normal growth conditions, although increased expression was detectable 0.5–72 h following a 42°C heat shock for 15–60 min. The intracellular iHsp70 level reached a maximum 8 h after onset of the heat shock, which correlated with its increased accumulation in nuclei. Inhibition of iHsp70 expression by quercetin showed that sustained activation of JNK (c‐Jun N‐terminal kinase) 2 and suppression of c‐Jun phosphorylation were responsible for myoblast death after heat shock. The data also demonstrate that activation of transcription factor c‐Jun depends mostly on JNK1, whereas JNK2 had higher affinity and was translocated to nuclei together with c‐Jun. We have also shown that the JNK signalling pathway is an upstream effect of iHsp70 expression. These findings provide further in‐depth understanding of the implication of the pro‐survival signalling kinases JNK1 and JNK2 and their target, c‐Jun, in expression of iHsp70 and regulation of myogenic stem cell survival and death mechanisms after heat shock. Mild heat shock before transplantation might be a way of improving myogenic stem cell survival.
First Report of Fusarium equiseti Causing Vascular Wilt of Cumin in India
Authors: Ramchandra S. , Bhatt P. N. 
Published: September 2012

Cumin (Cuminum cyminum) is one of the important spices in the world after black pepper. Cumin is mainly used in flavoring foods for its distinctive aroma and ayurvedic medicines. The production of cumin seeds in India is estimated to be around 0.15 million tons annually. Wilt symptoms were observed on field-grown cumin during the winter of 2009 and 2010. Diseased plants exhibited symptoms including wilted leaves, stunted growth, and eventually, death. In severe cases, approximately 65% of the plants in the field died. Isolations of the pathogen were made from the discolored tissues on potato dextrose agar (PDA) and Rose Bengal after disinfestations in 0.1% HgCl2 for 2 min and dipping in 70% ethanol for 10 s. Petri dishes were then incubated in complete darkness at 26°C for 7 days. Typical growth characters observed were development of abundant white aerial mycelium that turned peach orange by incubating under light. Microconidia were single-celled, hyaline, non-septate and ovoid, and ranged from 9.5 to 12.5 × 3.5 to 5.25 μm. Macroconidia were mostly two- to three-septate, slightly curved at apex, and ranged from 28.0 to 30.5 × 3.5 to 5.25 μm. The fungus was identified as Fusarium equiseti based on colony characters and spore morphology (3). The identity was further confirmed by the Fungal Identification Service, Mycology and Plant Pathology Group Agharkar Research Institute, Pune, India (Accession No. NFCCI-2157). The ITS (internal transcribed spacer) region of rDNA was amplified by polymerase chain reaction (PCR) with primers ITS1/ITS2 and sequenced (2). BLASTn analysis of the sequence obtained showed a 99.78% homology with F. equiseti at NCBI and FUSARIUM-ID v. 1.0 (1). The sequence was deposited at GenBank (Accession No. JN014954). Pathogenicity tests were conducted on 10 healthy 1-month-old seedlings of cumin in a moist chamber. Plants were separately inoculated in pots with sterilized soil and 10 ml of F. equiseti isolate spore suspension (107 conidia/ml) at 25°C for 7 to 10 days. Control plants were inoculated with sterile soil without spore suspension. Within 10 days, inoculated plants developed leaf wilt, stunted growth, discolored vascular tissue on stems, and finally died, which is similar to that observed in the field. Control seedlings were symptom free. Koch's postulates were fulfilled by reisolating the fungal pathogen, which was identified as F. equiseti causing vascular wilt on cumin reported in Israel (4). However; F. oxysporum f. sp. Cumini is the first reported vascular wilt of cumin. To our knowledge and on the basis of the literature, this the first report of vascular wilt of cumin caused by F. equiseti in India. References: (1) D. M. Geiser et al. Eur. J. Plant Pathol. 110:473, 2004. (2) M. Korabecna. In: Communicating Current Research and Educational Topics and Trends in Applied Microbiology, p. 783, 2007. (3) J. F. Leslie and B. A. Summerrell. The Fusarium Laboratory Manual. Blackwell Publishing, Ames, IA, 2006. (4) R. Reuveni. Plant Dis. 66:498, 1982.
First Report of Phytophthora megasperma Associated with Decline and Death of Common Walnut Trees in Italy
Authors: Belisario A. , Luongo L. , Galli M. , Vitale S. 
Published: September 2012

Common walnut (Juglans regia L.) is an important nut crop in Italy, which is the fifth largest producer of walnut in Europe. In recent years, walnut decline and subsequent death has increased in many Italian commercial orchards. In the summer of 2010, several declining trees were present in waterlogged area of a walnut orchard located in the Veneto region. Symptoms included sparse foliage, wilting, and shoot and branch dieback. By the next year, a larger area of about 1 ha with 20% of dead trees was present, and soil/root samples were subjected to azalea leaf baiting and successively cultured on PARBH medium (3). Isolates were identified as Phytophthora megasperma based on morphological characteristics (2) and DNA sequence analysis. Sporangia were 35.0 to 62.0 × 12.0 to 30.0 μm, nonpapillate, and noncaducous when produced in soil extract solution. Oogonia had an average diameter of 36 μm with mostly paragynous antheridia. Identity was confirmed by sequence comparison in NCBI database with 99% and 100% identity for internal transcribed spacer (ITS) and mitochondrial partial COI (4) for cytochrome oxidase subunit 1, respectively. The sequences of the isolate AB199 were deposited in GenBank with the accession nos. HE805270 and HE805269 for ITS and COI, respectively. Pathogenicity tests were conducted in the greenhouse on six 1-year-old walnut shoots with two inoculation points each. Mycelial plugs cut from the margins of actively growing 8-day-old cultures on PDA were inserted through the epidermis to the phloem. Controls were treated as described above except for inoculation with sterile PDA plugs. After inoculation, shoots were incubated in test tubes with sterile water for 1 week in the dark at 22 ± 2°C. Lesions were evident at the inoculation points. P. megasperma was consistently reisolated from the margin of symptomatic tissues. Controls remained symptomless. P. megasperma is a polyphagous, ubiquitarious Phytophthora species that attacks many crops and fruit species including walnut. Although several other species of Phytophthora have been reported from Italy (1), to the best of our knowledge, this is the first report of Phytophthora decline on common walnut in Italy caused by P. megasperma. References: (1) A. Belisario et al. Acta Hort. 705:401, 2006. (2) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society, St. Paul, MN, 1996. (3) G. C. Papavisas et al. Phytopathology 71:129, 1981. (4) G. P. Robideau et al. Mol. Ecol. Resour. 11:1002, 2011.