bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meiotic mutations in rye <i>Secale cereale</i> L.
Authors: Sosnikhina S.P. , Mikhailova E.I. , Tikholiz O.A. , Priyatkina S.N. , Smirnov V.G. , Dadashev S.Y. , Kolomiets O.L. , Bogdanov Y.F. 
Published: March 2005

Spontaneous meiotic mutations of winter rye <i>Secale cereale</i> L. (2n = 14) were revealed in inbred F<sub>2</sub> progenies, which were obtained by self-pollination of F<sub>1</sub> hybrids resulting from crosses of individual plants of cultivar Vyatka or weedy rye with plants of self-fertile inbred lines. The mutations cause partial or complete sterility, and are maintained in heterozygote condition. Six types of mutations were distinguished as the result of cytological analysis of meiosis and genetic analysis. (1) Plants with nonallelic asynaptic mutations <i>sy1</i> and <i>sy9</i> lacked bivalents in 96.8 and 67.0% metaphase I cells, respectively, formed only axial elements but not the mature synaptonemal complex (SC), and had defects in telomere clustering in early prophase I. (2) Weak asynaptic mutant <i>sy3</i> showed incomplete synapsis at the start of SC degradation at diplotene and lower chiasma number; yet only 2% meiocytes lacked bivalents in MI. (3) Mutations <i>sy2, sy6, sy7, sy8, sy10,</i> and <i>sy19</i> caused nonhomologous synapsis; i.e., a varying number of univalents and occasional multivalents were observed in MI, which was preceded by switches of pairing partners and fold-back synapsis at mid-prophase I. (4) Mutation <i>mei6</i> led to the formation of protrusions and minor branched structures of the SC lateral elements. (5) Allelic mutations <i>mei8</i> and <i>mei8-10</i> caused irregular chromatin condensation along the chromosome length in prophase I, which was accompanied by chromosome sticking and fragmentation in MI. (6) Allelic mutations <i>mei5</i> and <i>mei10</i> determined chromosome supercondensation, caused the disturbance of meiotic spindle assembly, arrested meiosis at various stages but did not affect formation of the pollen wall, thus arrested meiocytes got covered with the pollen wall. Analysis of double mutants revealed recessive epistatic interactions for some mutations; the epistatic group was <i>sy9 > sy1 > sy3 > sy19</i>. This reflects the sequence of meiotic events controlled by the corresponding genes. The expression of <i>sy2 </i>and <i>sy19</i> proved to be modified by additional genes. Most meiotic mutations found in rye have analogs in other plants.
The genome organization and diversification of maize and its allied species revisited: evidences from classical and FISH-GISH cytogenetic analysis
Authors: Poggio L. , Gonzalez G. , Confalonieri V. , Comas C. , Naranjo C.A. 
Published: March 2005

The present review summarizes our classical and molecular cytogenetic investigations in the genus <i>Zea</i>. The results obtained from the meiotic behavior analysis of <i>Zea</i> species and hybrids, confirm the amphiploid nature of all species in the genus, with a basic number of x = 5 chromosomes. All species with 2n = 20 are diploidized allotetraploids, whereas <i>Z. perennis</i> (2n = 40) is an allooctoploid with four genomes somewhat divergent from one another. These analyses also revealed the existence of postzygotic reproductive isolation among <i>Zea</i> species. Our studies using genomic in situ hybridization (GISH) provide evidence about the evolutionary relationships among maize and its allied species, and reveal remarkable genomic divergences. Particularly, knob sequences were not completely shared between taxa previously considered to be closely related. Our data strongly suggest that the teosinte <i>Z. mays parviglumis</i> is not the only progenitor of cultivated maize. Introgression of <i>Tripsacum</i> into cultivated maize cannot be discarded.
Biogeographic distribution of polyploidy and B chromosomes in the apomictic <i>Boechera holboellii</i> complex
Authors: Sharbel T.F. , Mitchell-Olds T. , Dobeš C. , Kantama L. , de Jong H. 
Published: March 2005

The <i>Boechera holboellii</i> complex comprises <i>B. holboellii</i> and <i>B. drummondii</i>, both of which can reproduce through sex or apomixis. Sexuality is associated with diploid individuals, whereas apomictic individuals are diploid or triploid and may additionally have B chromosomes. Using flow cytometry and karyotype analysis, we have shown that B chromosomes (a) occur in both diploid and triploid apomictic <i>B. holboellii,</i> (b) may occur in triploid <i>B. drummondii</i>, and (c) are dispensable for the plant. Both diploid and triploid karyotypes are found in multiple chloroplast haplotypes of both species, suggesting that triploid forms have originated multiple times during the evolution of this complex. B chromosome carriers are found in geographically and genetically distinct populations, but it is unknown whether the extra chromosomes are shared by common descent (single origin) or have originated via introgressive hybridization and repeated transitions from diploidy to triploidy. Diploid plants containing the Bs reproduce apomictically, suggesting that the supernumerary elements are associated with apomixis. Finally, our analyses of pollen size and viability suggest that irregular chromosome segregation in some triploid lineages may lead to the generation of diploid individuals which carry the B chromosomes.
Bigger or Better? The Role of Human Rights and Democracy in Determining Membership of the European Institutions
Authors: Duxbury Alison 
Published: March 2005

AbstractThis article traces the development of the role of human rights and democracy in determining admission to three European organizations: the Council of Europe, NATO and the EU. Despite the different functions that each organization performs, they have all assumed that prospective members must comply with human rights and democratic conditions. This is evident in both the organizations' constituent instruments and related membership documents, and also in the recent admission practice of the three organizations. But the membership practice also indicates that since their establishment the organizations have not always applied these conditions rigorously – thus there is a tension between the organizations' desire for homogenous universality (getting better) and heterogeneous universality (getting bigger). The admission practice also reveals a number of problems with the use of human rights and democratic criteria, including inconsistencies in the application of the criteria between applicants and existing members of the same organization, and inconsistencies in the application of the shared criteria across the three organizations. In the end, the development of the common membership criteria of human rights and democracy highlights both a degree of flexibility in admission decisions, as well as a progressive change in the functions of each organization.
The Coupled Manifold*
Authors: Navarra A. , Tribbia J. 
Published: March 2005

Abstract
A new method is presented to detect the portion of variability connected between two climatic fields. The method is a realization of the Procrustes problem, and it is a generalization of methods for analysis of variance such as the singular value decomposition (SVD) or canonical correlation analysis (CCA). The Procrustes formulation offers a general framework to link together variance analysis methods, and regression methods, including as special cases SVD and CCA.
Using this approach two fields can be divided into a subspace where variations of one field are connected to variations of the other field, the coupled manifold, and a subspace where variations are independent, the free manifold. The unified approach can be applied to prescribed SST experiments, in which case it recovers consistent results with other methods designed to identify the forced portion of variance, but it can now be extended also to the coupled case or to observations.
Some examples from prescribed SST simulation experiments and observations are discussed.
Equatorial Superrotation and the Factors Controlling the Zonal-Mean Zonal Winds in the Tropical Upper Troposphere
Authors: Kraucunas Ian , Hartmann Dennis L. 
Published: March 2005

Abstract
The response of the zonal-mean zonal winds in the tropical upper troposphere to thermal forcing in the Tropics is studied using an idealized general circulation model with 18 vertical levels and simplified atmospheric physics. The model produces a conventional general circulation, with deep easterly flow over the equator, when integrated using zonally invariant and hemispherically symmetric boundary conditions, but persistent equatorial superrotation (westerly zonal-mean flow over the equator) is obtained when steady longitudinal variations in diabatic heating are imposed at low latitudes. The superrotation is driven by horizontal eddy momentum fluxes associated with the stationary planetary wave response to the applied tropical heating. The strength of the equatorial westerlies is ultimately limited by vertical steady eddy momentum fluxes, which are downward in the tropical upper troposphere, and by the zonally averaged circulation in the meridional plane, which erodes the mean westerly shear via vertical advection.
The transition to superrotation can be prevented by specifying offsetting zonally invariant heating and cooling anomalies on either side of the equator to create a “solstitial” basic state with a single dominant Hadley cell straddling the equator. Superrotation is restricted in the solstitial climate because the strength of the mean meridional overturning is enhanced, which increases the efficiency of vertical advection, and because the cross-equatorial flow in the upper troposphere provides an easterly zonal acceleration that offsets some of the momentum flux convergence associated with tropical eddy heating. The cross-equatorial flow aloft also reduces the stationary planetary wave response in the summer hemisphere. These results suggest that hemispheric asymmetry in the mean meridional circulation is responsible for maintaining the observed mean easterly flow in the tropical upper troposphere against the westerly torques associated with tropical wave sources.
Extratropical Dry-Air Intrusions into the West African Monsoon Midtroposphere: An Important Factor for the Convective Activity over the Sahel
Authors: Roca Rémy , Lafore Jean-Philippe , Piriou Catherine , Redelsperger Jean-Luc 
Published: March 2005

Abstract
This paper investigates the relationship between large-scale dynamics, water vapor, and organized convection over West Africa. Making use of a simplified condensation hypothesis, a back-trajectory model fed by NCEP-analyzed winds is used to reconstruct the midtropospheric humidity field over Africa during July to August 1992. The approach documents both the moisture content and the origin of the air masses. Meteosat satellite infrared imagery is used to characterize the convective systems.
A case study analysis reveals that very dry air patches (RH &lt; 5%) are located in the immediate midtropospheric environment of a typical squall line. Such dry-air structures are shown to originate in the upper levels (200–250 hPa) on the anticyclonic side of the polar jet stream at 50°N. Focusing on the Sahel region, dry events are isolated using the time series of the 500-hPa relative humidity distribution during the monsoon period. These dry events are shown to be composed of extratropical air. Composite analysis of the convective activity indicator exhibits a strong positive association between dry intrusions and convection on the eastern side of the Sahelian region. Organized convective systems that are fast moving and long lasting are more likely over this region when a dry intrusion is present. This coincides with the well-established theory that midtropospheric dry air, when combined with sufficient wind shear, can maintain and intensify previously triggered deep convection through rain evaporation that feeds the cold pools, especially within squall lines. This paper suggests that the extratropical dry-air intrusions modulate the occurrence and duration of convective systems and, therefore, the mode of variability of rainfall over West Africa during the monsoon.
The Theory of Ice Nucleation by Heterogeneous Freezing of Deliquescent Mixed CCN. Part II: Parcel Model Simulation
Authors: Khvorostyanov Vitaly I. , Curry Judith A. 
Published: March 2005

AbstractThe new theory of ice nucleation by heterogeneous freezing of deliquescent mixed cloud condensation nuclei (CCN) presented in Part I is incorporated into a parcel model with explicit water and ice bin microphysics to simulate the process of ice nucleation under transient thermodynamic conditions. Simulations are conducted over the temperature range −4° to −60°C, with vertical velocities varying from 1 to 100 cm s−1, for varying initial relative humidities and aerosol characteristics. These simulations show that the same CCN that are responsible for the drop nucleation may initiate crystal nucleation and can be identified as ice nuclei (IN) when crystals form. The simulated nucleation rates and concentrations of nucleated crystals depend on temperature and supersaturation simultaneously, showing good agreement with observations but with noticeable differences when compared with classical temperature-only and supersaturation-only parameterizations. The kinetics of heterogeneous ice nucleation exhibits a negative feedback via water supersaturation, whereby ice nucleation depends on the water supersaturation that is diminished by ice crystal diffusional growth. This feedback is stronger than the corresponding feedback for drop nucleation, and may explain discrepancies between observed ice nuclei concentrations and ice crystal concentrations, the very small fraction of CCN that may serve as IN, and the much smaller crystal concentrations as compared to drop concentrations. The relative importance of heterogeneous versus homogeneous nucleation is examined for a variety of cloud conditions. Based on these calculations, a simple parameterization for ice crystal concentration is suggested for use in cloud models and large-scale models.
Small-Scale Drop-Size Variability: Empirical Models for Drop-Size-Dependent Clustering in Clouds
Authors: Marshak Alexander , Knyazikhin Yuri , Larsen Michael L. , Wiscombe Warren J. 
Published: March 2005

Abstract
By analyzing aircraft measurements of individual drop sizes in clouds, it has been shown in a companion paper that the probability of finding a drop of radius r at a linear scale l decreases as lD(r), where 0 ≤ D(r) ≤ 1. This paper shows striking examples of the spatial distribution of large cloud drops using models that simulate the observed power laws. In contrast to currently used models that assume homogeneity and a Poisson distribution of cloud drops, these models illustrate strong drop clustering, especially with larger drops. The degree of clustering is determined by the observed exponents D(r). The strong clustering of large drops arises naturally from the observed power-law statistics. This clustering has vital consequences for rain physics, including how fast rain can form. For radiative transfer theory, clustering of large drops enhances their impact on the cloud optical path. The clustering phenomenon also helps explain why remotely sensed cloud drop size is generally larger than that measured in situ.
A Refined Method of Parameterizing Absorption Coefficients among Multiple Gases Simultaneously from Line-by-Line Data
Authors: Jacobson Mark Z. 
Published: March 2005

Abstract
An extension of the correlated-k distribution method that uses spectral-mapping techniques was derived to parameterize line-by-line absorption coefficients for multiple gases simultaneously for use in three-dimensional atmospheric models. In a variation from previous correlation techniques, this technique ensures exact correlation of absorption frequencies within a probability interval for all gases through all layers of the atmosphere when multiple gases are considered. The technique is physical since, in reality, gases are correlated in wavelength space. The technique, referred to as the “multiple-absorber correlated-k distribution spectral-mapping method,” was found to be accurate to &lt;0.7% of incident radiation for 16 probability intervals per wavelength interval, integrated over 0.4–1000-μm wavelengths and accounting for 11 absorbing gases simultaneously and multiple layers, compared with an exact line-by-line solution. A method was also derived to reduce the number of probability intervals required for a radiative transfer solution without suffering the same inaccuracy as merely reducing the number of probability intervals when parameterizing the absorption coefficient. The new coefficients were tested in a global model, and results were compared with mean thermal-IR irradiance data.
Distributed Forcing of Forecast and Assimilation Error Systems
Authors: Farrell Brian F. , Ioannou Petros J. 
Published: March 2005

AbstractTemporally distributed deterministic and stochastic excitation of the tangent linear forecast system governing forecast error growth and the tangent linear observer system governing assimilation error growth is examined. The method used is to determine the optimal set of distributed deterministic and stochastic forcings of the forecast and observer systems over a chosen time interval. Distributed forcing of an unstable system addresses the effect of model error on forecast error in the presumably unstable forecast error system. Distributed forcing of a stable system addresses the effect on the assimilation of model error in the presumably stable data assimilation system viewed as a stable observer. In this study, model error refers both to extrinsic physical error forcing, such as that which arises from unresolved cumulus activity, and to intrinsic error sources arising from imperfections in the numerical model and in the physical parameterizations.
Reexamining the Near-Core Radial Structure of the Tropical Cyclone Primary Circulation: Implications for Vortex Resiliency
Authors: Mallen Kevin J. , Montgomery Michael T. , Wang Bin 
Published: March 2005

Abstract
Recent theoretical studies, based on vortex Rossby wave (VRW) dynamics, have established the importance of the radial structure of the primary circulation in the response of tropical cyclone (TC)–like vortices to ambient vertical wind shear. Linear VRW theory suggests, in particular, that the degree of broadness of the primary circulation in the near-core region beyond the radius of maximum wind strongly influences whether a tilted TC vortex will realign and resist vertical shear or tilt over and shear apart. Fully nonlinear numerical simulations have verified that the vortex resiliency is indeed sensitive to the initial radial structure of the idealized vortex. This raises the question of how well the “true” nature of a TC’s primary circulation is represented by idealized vortices that are commonly used in some theoretical studies.
In this paper the swirling wind structure of TCs is reexamined by utilizing flight-level observations collected from Atlantic and eastern Pacific storms during 1977–2001. Hundreds of radial profiles of azimuthal-mean tangential wind and relative vorticity are constructed from over 5000 radial flight leg segments and compared with some standard idealized vortex profiles. This analysis reaffirms that real TC structure in the near-core region is characterized by relatively slow tangential wind decay in conjunction with a skirt of significant cyclonic relative vorticity possessing a negative radial gradient. This broadness of the primary circulation is conspicuously absent in some idealized vortices used in theoretical studies of TC evolution in vertical shear. The relationship of the current findings to the problem of TC resiliency is discussed.
Optimal Perturbations in the Eady Model: Resonance versus PV Unshielding
Authors: de Vries H. , Opsteegh J. D. 
Published: March 2005

Abstract
Using a nonmodal decomposition technique based on the potential vorticity (PV) perspective, the optimal perturbation or singular vector (SV) of the Eady model without upper rigid lid is studied for a kinetic energy norm. Special emphasis is put on the role of the continuum modes (CMs) in the structure of the SV, and on the importance of resonance to the SV evolution. The basis for the SV is formed by a number of nonmodal structures, each consisting of a superposition of one CM and one edge wave, such that the initial surface potential temperature (PT) is zero. These nonmodal structures are used as PV building blocks to construct the SV. The motivation for using a nonmodal approach is that no attempt has been made so far to include the CM residing at the steering level of the surface edge wave in the perturbation, although it is known that this CM is in linear resonance with the surface edge wave.
Experiments with one PV building block in the initial disturbance show that the SV growth is dominated by the resonance effect except for small optimization times (less than 1 day), in which case the unshielding of PV and surface PT dominates the growth of the SV. The PV–PT unshielding provides additional growth to the SV and this explains the observation that the PV resides above the resonant level.
More PV building blocks are added to include PV unshielding as a third growth mechanism. Which of the three mechanisms dominates during the SV evolution depends on the region of interest (interior or surface), as well as on the optimization time and on the number of building blocks used. At the surface, resonance plays a dominant role even when a large number of building blocks is used and relatively small optimization times are used. For the interior of the domain, PV unshielding becomes the dominant growth mechanism when more than two PV building blocks are used. With increasing optimization times, the PV distribution of the SV becomes increasingly more concentrated near the steering level of the edge wave. This concentration of PV is explained by the enhanced importance of resonance for long optimization times as compared to short optimization times.
Computational verification of protein-protein interactions by orthologous co-expression
Authors: Tirosh Itay , Barkai Naama 
Published: March 2005

Abstract
Background
High-throughput methods identify an overwhelming number of protein-protein interactions. However, the limited accuracy of these methods results in the false identification of many spurious interactions. Accordingly, the resulting interactions are regarded as hypothetical and computational methods are needed to increase their confidence. Several methods have recently been suggested for this purpose including co-expression as a confidence measure for interacting proteins, but their performance is still quite poor.

Results
We introduce a novel computational method for verification of protein-protein interactions based on the co-expression of orthologs of interacting partners. The performance of our method is analysed using known S. cerevisiae interactions, and is shown to overcome limitations of previous methods. We present specific examples of known and putative interactions that are detected by our method and not by previous methods, and suggest that they represent transient interactions that might have been conserved and stabilized in other species.

Conclusion
Co-expression of orthologous protein-pairs can be used to increase the confidence of hypothetical protein-protein interactions in S. cerevisiae as well as in other species. This approach may be especially useful for species with no available expression profiles and for transient interactions.