bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability of backwater‐influenced river bifurcations: A study of the Mississippi‐Atchafalaya system
Authors: Edmonds D. A.
Published: March 2012

In this paper I use numerical modeling to show that the hydraulic backwater profile creates a feedback that may stabilize river bifurcations. The numerical model simulates flow and sediment transport in the Mississippi‐Atchafalaya River system without the Old River Control Structure. The results show that bifurcation evolution strongly depends on the discharge upstream of the bifurcation. At upstream discharges greater than 12600 m3 s−1 the Atchafalaya River discharge increases through time at the expense of the Mississippi River. Interestingly, at upstream discharges lower than 12600 m3 s−1 the opposite occurs and the Mississippi River discharge increases at the expense of the Atchafalaya River. The capture direction changes because the backwater profile of each river varies enough at high and low discharge to invert the water surface slope ratio. These results suggest that the capture direction would change at high and low flow, which would have a stabilizing effect by preventing the runaway growth of one channel. Accounting for this, I calculate that in the absence of the Old River Control Structure capture would not happen catastrophically, but rather the Atchafalaya River would capture the Mississippi River in ∼300 years from present day.
Processes controlling the 2010 Eyjafjallajökull explosive eruption
Authors: Borisova Anastassia Y. , Toutain Jean‐Paul , Stefansson Andri , Gouy Sophie , de Parseval Philippe
Published: March 2012

To constrain the temporal evolution of the fluid‐magma system responsible for the 2010 Eyjafjallajökull eruption (20 March to 20 May, 2010, Southern Iceland), we investigated the volatile, major, trace element, and Sr‐Nd‐Pb isotopic compositions of bulk lapilli and ash samples representing different stages of the eruption. In addition, we analyzed ash leachates and volcanic plume‐derived aerosols sampled over Southern Europe in early May 2010. Available remote‐sensing data for the total mass of SO2 liberated in the 2010 eruption, together with data obtained in this study, suggest that the high explosivity of the 2010 sub‐plinian Eyjafjallajökull eruption was caused by saturation of the pre‐eruptive hybrid trachyandesitic magma with aqueous fluid. We hypothesize that the bulk of the aqueous fluid had been dissolved in the trachydacitic melt at least since the eruption of 1821–1823. The trachydacitic melt was enriched in volatiles, large‐ion lithophile elements, and high field strength elements, a composition similar to that of oceanic sediments. The Sr‐Nd‐Pb isotopic data obtained in this study, combined with existing O isotopic data on bulk 2010 Eyjafjallajökull lapilli and ashes, demonstrate that this melt enrichment was due to its primary source being hydrous oceanic lithosphere entrained in a deep mantle plume rather than shallow hydrothermally altered crust. The hypothesized strong crystal fractionation of plume‐derived mafic melts (crystallized fraction >90%) from an enriched mantle source can explain the observed high explosivity of silicic and hybrid Icelandic magmas, especially those of the southeastern volcanic zone (Eyjafjallajökull, Katla, and Hekla).
Endogenous, or therapeutically induced, type I interferon responses differentially modulate Th1/Th17‐mediated autoimmunity in the CNS
Authors: Kalinke Ulrich , Prinz Marco
Published: March 2012

Different viruses trigger pattern recognition receptor systems, such as Toll‐like receptors or cytosolic RIG‐I like helicases (RLH), and thus induce early type I interferon (IFN‐I) responses. Such responses may confer protection until adaptive immunity is activated to an extent that the pathogen can be eradicated. Interestingly, the same innate immune mechanisms that are relevant for early pathogen defense have a role in ameliorating experimental autoimmune encephalomyelitis (EAE), a rodent model of human multiple sclerosis. We and others found that mice devoid of a component of the IFN‐I receptor (Ifnar1−/−) showed significantly enhanced autoimmune disease of the central nervous system (CNS). A detailed analysis revealed that in wild‐type mice IFN‐I triggering of myeloid cells was instrumental in reducing brain damage. A more recent study indicated that similar to Ifnar1−/− mice, RLH‐signaling‐deficient mice showed enhanced autoimmune disease of the CNS as well. Moreover, when peripherally treated with synthetic RLH ligands wild‐type animals with EAE disease showed reduced clinical scores. Under such conditions, IFN‐I receptor triggering of dendritic cells had a crucial role. The therapeutic effect of treatment with RLH ligands was associated with negative regulation of Th1 and Th17 T‐cell responses within the CNS. These experiments are consistent with the hypothesis that spatiotemporal conditions of, and cell types involved in, disease‐ameliorating IFN‐I responses differ significantly, depending on whether they were endogenously induced in the context of EAE pathogenesis within the CNS or upon therapeutic RLH triggering in the periphery. It is attractive to speculate that RLH triggering represents a new strategy to treat multiple sclerosis by stimulating endogenous immunoregulatory IFN‐I responses.
Identification of transcription factor genes and their correlation with the high diversity of Stramenopiles
Authors: Buitrago Francisco , Restrepo Silvia , Riaño-Pachón Diego
Published: March 2012

In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the regulation of specific traits for some Stramenopile species.
Bryophyte communities and seston in a karst stream (Jankovac Stream, Papuk Nature Park, Croatia)
Authors: Špoljar Maria , Dražina Tvrtko , Ostojić Ana , Miliša Marko , Udovič Marija Gligora , Štafa Dagmar
Published: March 2012

An investigation into bryophyte communities in karst Jankovac Stream (Papuk Nature Park, Croatia) was carried out once a month from July 2008 to June 2009. Samples were taken from two lotic microhabitats: (i) Jankovac Spring (JS), a hypocrenal habitat with dense bryophyte clusters (90% bottom cover) and (ii) Jankovac Waterfall (JW), with scattered bryophyte clusters (50% bottom cover). At the same time, seston samples were collected during the spring as the source site and after the JW, as the outflow site. The goals of this study were to understand the (i) algal, protozoan and metazoan bryophyte community assemblages in these two lotic microhabitats, (ii) influence of environmental factors on the structuring of the bryophyte community and (iii) structure of seston along the longitudinal profile. A total of 172 taxa were determined: 68 algae, 55 protozoa, 24 meiofauna and 25 macroinvertebrates. Statistically significant differences between two microhabitats differing in percentage of bryophyte cover were established testing 13 environmental parameters. In dense bryophyte clusters, community structure was determined by flow velocity and pH, and macroinvertebrates achieved higher diversity and abundance. On the contrary, in scattered bryophyte coverage algae, protozoa and meiofauna reached higher abundance and diversity governed by the amount of suspended organic matter and epiphyton. In contrast to previous studies, the inverse ratio of community diversity and abundanceversuspercentage of bryophyte cover was established. We assume this to be the result of an enrichment of the scattered bryophyte clusters by upstream seston. Additionally, the effects of anthropogenic hydromorphological disturbance are reflected in macroinvertebrate diversity and abundance reduction.
Electronic origin of the negligible magnetostriction of an electric steel Fe1-xSix alloy: A density-functional study
Authors: Odkhuu Dorj , Seok Yun Won , Cheol Hong Soon
Published: March 2012

To understand the negligible magnetostriction of Fe-Si alloys used as cores in electric transformers or motors, density-functional calculations were performed on the tetragonal magnetostriction coefficient, λ001, of Fe1-xSix (x ≤ 0.25) alloys as a function of x using the highly precise all-electron full-potential linearized augmented plane-wave method. It was found that the calculated magnetostriction coefficients closely reproduced experimental trends and the negligible magnetostriction near x = 0.111 originated from the mixed phases of A2, B2, and D03; each different atomic type of Fe of Fe0.889Si0.111 has a small and opposite contribution to the magnetostriction.
Period adding cascades: Experiment and modeling in air bubbling
Authors: Augusto Cardoso Pereira Felipe , Colli Eduardo , Carlos Sartorelli José
Published: March 2012

Period adding cascades have been observed experimentally/numerically in the dynamics of neurons and pancreatic cells, lasers, electric circuits, chemical reactions, oceanic internal waves, and also in air bubbling. We show that the period adding cascades appearing in bubbling from a nozzle submerged in a viscous liquid can be reproduced by a simple model, based on some hydrodynamical principles, dealing with the time evolution of two variables, bubble position and pressure of the air chamber, through a system of differential equations with a rule of detachment based on force balance. The model further reduces to an iterating one-dimensional map giving the pressures at the detachments, where time between bubbles come out as an observable of the dynamics. The model has not only good agreement with experimental data, but is also able to predict the influence of the main parameters involved, like the length of the hose connecting the air supplier with the needle, the needle radius and the needle length.
Ab initio many-electron study for the low-lying states of the alkali hydride cations in the adiabatic representation
Authors: Yan Lingling , Qu Yizhi , Liu Chunhua , Wang Jianguo , Buenker Robert J.
Published: March 2012

An ab initio multireference single- and double-excitation configuration interaction (CI) study is carried out for the ground and excited electronic states of alkali-hydride cations (LiH+, NaH+, KH+, RbH+, and CsH+). For all alkali-metal atoms, the first inner-shell and valence electrons (nine active electrons, three for Li) are considered explicitly in the ab initio self-consistent-field and CI calculations. The adiabatic potential energy curves, radial and rotational couplings are calculated and presented. Short-range (∼3 a.u.) potential wells produced by the excitation of the inner-shell electrons are found. The depths of the inner potential wells are much greater than those of the outer wells for the CsH+ system. The computed spectroscopic constants for the long-range potential well of the 2 2Σ+ state are very close to the available theoretical and experimental data. The electronic states of alkali-hydrogen cations are also compared with each other, it is found that the positions of the potential wells shift to larger internuclear distances gradually, and the depths of these potential wells become greater with increasing alkali-metal atomic number. The relationships between structures of the radial coupling matrix elements and the avoiding crossings of the potential curves are analyzed. From NaH+ to CsH+, radial coupling matrix elements display more and more complex structures due to the gradual decrease of energy separations for avoided crossings. Finally, the behavior of some rotational couplings is also shown.
Positron scattering from the cyclic ethers oxirane, 1,4-dioxane, and tetrahydropyran
Authors: Zecca A. , Trainotti E. , Chiari L. , Bettega M. H. F. , Sanchez S. d'A , Varella M. T. do N. , Lima M. A. P. , Brunger M. J.
Published: March 2012

In this paper we report original measurements of total cross sections (TCSs) for positron scattering from the cyclic ethers oxirane (C2H4O), 1,4-dioxane (C4H8O2), and tetrahydropyran (C5H10O). The present experiments focus on the low energy range from ∼0.2  to  50 eV, with an energy resolution smaller than 300 meV. This study concludes our systematic investigation into TCSs for a class of organic compounds that can be thought of as sub-units or moieties to the nucleotides in living matter, and which as a consequence have become topical for scientists seeking to simulate particle tracks in matter. Note that as TCSs specify the mean free path between collisions in such simulations, they have enjoyed something of a recent renaissance in interest because of that application. For oxirane, we also report original Schwinger multichannel elastic integral cross section (ICS) calculations at the static and static plus polarisation levels, and with and without Born-closure that attempts to account for the permanent dipole moment of C2H4O. Those elastic ICSs are computed for the energy range 0.5–10 eV. To the best of our knowledge, there are no other experimental results or theoretical calculations against which we can compare the present positron TCSs. However, electron TCSs for oxirane (also known as ethylene oxide) and tetrahydropyran do currently exist in the literature and a comparison to them for each species will be presented.
Small-scale dynamo action in multi-scale magnetohydrodynamic and micro-turbulence
Authors: Li Jiquan , Kishimoto Y.
Published: March 2012

Nonlinear interplay between resistive magnetohydrodynamic (MHD) magnetic island and drift wave micro-turbulence is investigated using direct Landau-fluid simulations. A twisting oscillation of magnetic island associated with the driving force of micro-turbulence is observed, which is referred to as magnetic island seesaw. In the initiating phase of the seesaw oscillation, small-scale current and magnetic field fluctuations increase dramatically while the magnetic induction grows exponentially at small-scales corresponding to the spatial scale of micro-turbulence, showing a small-scale dynamo action. A minimal model consisting of reduced MHD turbulence and a micro-instability is proposed to elucidate the underlying mechanism. It is identified that the island seesaw is driven by a net oscillatory electromagnetic torque, which results from small-scale dynamo-generated current and magnetic field. The dynamo mechanism may offer an important energy exchange channel between MHD and micro-turbulence in magnetic fusion plasmas.
Characterisation of cellulose and hemicellulose digestion in land crabs with special reference to Gecarcoidea natalis
Authors: Allardyce Benjamin J. , Linton Stuart M.
Published: March 2012

This article reviews the current knowledge of cellulose and hemicellulose digestion by herbivorous land crabs using the gecarcinid Gecarcoidea natalis as a model species for this group. Cellulose digestion in the gecarcinids is hypothesised to require mechanical fragmentation and enzymatic hydrolysis. Mechanical fragmentation is achieved by the chelae, mandibles and gastric mill, which reduce the material to particles less than 53 µm. The gastric mill shows adaptations towards a plant diet; in particular, there are transverse ridges on the medial and lateral teeth and ventral cusps on the lateral teeth that complement and interlock to provide efficient cutting surfaces. Enzymatic hydrolysis of cellulose and hemicellulose is achieved through cellulase and hemicellulase enzymes. In the gecarcinids, 2–3 endo-β-1,4-glucanases, one β-glucohydrolase and a laminarinase have been identified. The endo-β-1,4-glucanases are multifunctional, with both endo-β-1,4-glucanase and lichenase activity. Complete cellulose hydrolysis is achieved through the synergistic action of the endo-β-1,4-glucanase and β-glucohydrolase. The evidence for the endogenous production of the cellulase and hemicellulase enzymes, their evolutionary origin and possible evolution in invertebrates as they colonised land is also discussed.
Histological study of gonadal development and sex differentiation in Salvelinus fontinalis under Tasmanian climate conditions
Authors: Fatima Shafaq , Adams Mark , Wilkinson Ryan
Published: March 2012

This study describes the developmental process of gonads in brook trout from 0 degree days post-hatch (°dph) until completion of sex differentiation (3354°dph). Gonadal development was divided into undifferentiated (0–2013°dph) and differentiated phases (2769–3354°dph). Fertilised eggs (n = 1000) were incubated at 9.5−10°C until hatching at 66 days post-fertilisation (dpf). A total of 20% of alevins sampled on 0°dph were found with unpaired and undifferentiated gonads, indicating that gonadal development commenced before hatch. Initially, undifferentiated gonads contained stromal tissue and few primordial gonadal cells (PGC) (n = 2–5). During the undifferentiated phase, gonads increased in size and proliferative activity of the PGC increased their number (n = 15–22). The differentiated phase commenced with the appearance of sex differentiation at 2769°dph where gonads could be clearly differentiated as ovaries and presumptive testes. Ovaries were identified by the presence of oogonia while presumptive testes contained spermatogonia, vena comittis and a proximal network of cavities. Both ovaries and testes underwent further differentiation until the end of this phase (3354°dph). Oogonia were transformed into primary oocytes while spermatogonial cysts were observed in testes. However, differentiation of steroidogenic cells could not be observed. Direct sex differentiation was found in this study as undifferentiated gonads directly developed into testes and ovaries with anatomical differentiation preceding cytological differentiation. This study confirms previous studies that the prehatch period should be targeted when attempting to produce future monosex populations via indirect sex reversal using androgen treatment.
Localization of a toxic form of superoxide dismutase 1 protein to pathologically affected tissues in familial ALS
Authors: Brotherton Terrell E. , Li Yingjie , Cooper Deborah , Gearing Marla , Julien Jean-Pierre , Rothstein Jeffrey D. , Boylan Kevin , Glass Jonathan D.
Published: March 2012

Mutations in the gene encoding superoxide dismutase 1 (SOD1) account for about 20% of the cases of familial amyotrophic lateral sclerosis (fALS). It is not known how the mutant protein causes disease, or why only a subset of cell types (motor neurons) are targeted. The aggregation and misfolding of mutant SOD1 are implicated in disease pathogenesis in both animal models and humans. We used a monoclonal antibody, C4F6, which specifically reacts with mutant and/or “misfolded” SOD1, to investigate the regional distribution of mutant SOD1 protein in rodent and human tissues. C4F6 reacted only with mutant SOD1 and showed remarkable selectivity for disease-affected tissues and cells. Tissue not affected by disease but containing high levels of mutant protein (sensory neurons) did not stain with C4F6. Additionally, C4F6 intensely stained some motor neurons while leaving adjacent motor neurons unstained. Although C4F6 was generated against the G93A SOD1 mutant, it also recognized other SOD1 mutants. In human autopsy tissues from patients carrying SOD1 mutations, C4F6 identified skein-like intracellular inclusions in motor neurons, similar to those seen in rodents, and again stained only a subset of motor neurons. In spinal cords from patients with sporadic ALS, other neurodegenerative diseases, and normal controls, C4F6-immunoreactive inclusions were not detected, but the antibody did reveal diffuse immunostaining of some spinal motor neurons. The ability of C4F6 to differentiate pathologically affected tissue in mutant SOD1 ALS rodent models and humans, specifically motor neuron populations, suggests that this antibody may recognize a “toxic” form of the mutant SOD1 protein.
Origin of excitation underlying locomotion in the spinal circuit of zebrafish
Authors: Eklöf-Ljunggren Emma , Haupt Sabine , Ausborn Jessica , Dehnisch Ivar , Uhlén Per , Higashijima Shin-ichi , El Manira Abdeljabbar
Published: March 2012

Neural circuits in the spinal cord transform instructive signals from the brain into well-coordinated locomotor movements by virtue of rhythm-generating components. Although evidence suggests that excitatory interneurons are the essence of locomotor rhythm generation, their molecular identity and the assessment of their necessity have remained unclear. Here we show, using larval zebrafish, that V2a interneurons represent an intrinsic source of excitation necessary for the normal expression of the locomotor rhythm. Acute and selective ablation of these interneurons increases the threshold of induction of swimming activity, decreases the burst frequency, and alters the coordination of the rostro–caudal propagation of activity. Thus, our results argue that V2a interneurons represent a source of excitation that endows the spinal circuit with the capacity to generate locomotion.
Effect of channel mutations on the uptake and release of the retinal ligand in opsin
Authors: Piechnick Ronny , Ritter Eglof , Hildebrand Peter W. , Ernst Oliver P. , Scheerer Patrick , Hofmann Klaus Peter , Heck Martin
Published: March 2012

In the retinal binding pocket of rhodopsin, a Schiff base links the retinal ligand covalently to the Lys296 side chain. Light transforms the inverse agonist 11-
cis
-retinal into the agonist all-
trans
-retinal, leading to the active Meta II state. Crystal structures of Meta II and the active conformation of the opsin apoprotein revealed two openings of the 7-transmembrane (TM) bundle towards the hydrophobic core of the membrane, one between TM1/TM7 and one between TM5/TM6, respectively. Computational analysis revealed a putative ligand channel connecting the openings and traversing the binding pocket. Identified constrictions within the channel motivated this study of 35 rhodopsin mutants in which single amino acids lining the channel were replaced. 11-
cis
-retinal uptake and all-
trans
-retinal release were measured using UV/visible and fluorescence spectroscopy. Most mutations slow or accelerate both uptake and release, often with opposite effects. Mutations closer to the Lys296 active site show larger effects. The nucleophile hydroxylamine accelerates retinal release 80 times but the action profile of the mutants remains very similar. The data show that the mutations do not probe local channel permeability but rather affect global protein dynamics, with the focal point in the ligand pocket. We propose a model for retinal/receptor interaction in which the active receptor conformation sets the open state of the channel for 11-
cis
-retinal and all-
trans
-retinal, with positioning of the ligand at the active site as the kinetic bottleneck. Although other G protein-coupled receptors lack the covalent link to the protein, the access of ligands to their binding pocket may follow similar schemes.
Distributed representation of chemical features and tunotopic organization of glomeruli in the mouse olfactory bulb
Authors: Ma Limei , Qiu Qiang , Gradwohl Stephen , Scott Aaron , Yu Elden Q. , Alexander Richard , Wiegraebe Winfried , Yu C. Ron
Published: March 2012

In the mammalian brain, similar features of the sensory stimuli are often represented in proximity in the sensory areas. However, how chemical features are represented in the olfactory bulb has been controversial. Questions have been raised as to whether specific chemical features of the odor molecules are represented by spatially clustered olfactory glomeruli. Using a sensitive probe, we have analyzed the glomerular response to large numbers of odorants at single glomerulus resolution. Contrary to the general view, we find that the representation of chemical features is spatially distributed in the olfactory bulb with no discernible chemotopy. Moreover, odor-evoked pattern of activity does not correlate directly with odor structure in general. Despite the lack of spatial clustering or preference with respect to chemical features, some structurally related odors can be similarly represented by ensembles of spatially distributed glomeruli, providing an explanation of their perceptual similarity. Whereas there is no chemotopic organization, and the glomeruli are tuned to odors from multiple classes, we find that the glomeruli are hierarchically arranged into clusters according to their odor-tuning similarity. This tunotopic arrangement provides a framework to understand the spatial organization of the glomeruli that conforms to the organizational principle found in other sensory systems.
Fluorescence microscopy for simultaneous observation of 3D orientation and movement and its application to quantum rod-tagged myosin V
Authors: Ohmachi Masashi , Komori Yasunori , Iwane Atsuko H. , Fujii Fumihiko , Jin Takashi , Yanagida Toshio
Published: March 2012

Single molecule fluorescence polarization techniques have been used for three-dimensional (3D) orientation measurements to observe the dynamic properties of single molecules. However, only few techniques can simultaneously measure 3D orientation and position. Furthermore, these techniques often require complex equipment and cumbersome analysis. We have developed a microscopy system and synthesized highly fluorescent, rod-like shaped quantum dots (Q rods), which have linear polarizations, to simultaneously measure the position and 3D orientation of a single fluorescent probe. The optics splits the fluorescence from the probe into four different spots depending on the polarization angle and projects them onto a CCD camera. These spots are used to determine the 2D position and 3D orientation. Q rod orientations could be determined with better than 10° accuracy at 33 ms time resolution. We applied our microscopy and Q rods to simultaneously measure myosin V movement along an actin filament and rotation around its own axis, finding that myosin V rotates 90° for each step. From this result, we suggest that in the two-headed bound state, myosin V necks are perpendicular to one another, while in the one-headed bound state the detached trailing myosin V head is biased forward in part by rotating its lever arm about its own axis. This microscopy system should be applicable to a wide range of dynamic biological processes that depend on single molecule orientation dynamics.
Feline morbillivirus, a previously undescribed paramyxovirus associated with tubulointerstitial nephritis in domestic cats
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Wong Beatrice H. L. , Fan Rachel Y. Y. , Wong Annette Y. P. , Zhang Anna J. X. , Wu Ying , Choi Garnet K. Y. , Li Kenneth S. M. , Hui Janet , Wang Ming , Zheng Bo-Jian , Chan K. H. , Yuen Kwok-Yung
Published: March 2012

We describe the discovery and isolation of a paramyxovirus, feline morbillivirus (FmoPV), from domestic cat (
Felis catus
). FmoPV RNA was detected in 56 (12.3%) of 457 stray cats (53 urine, four rectal swabs, and one blood sample) by RT-PCR. Complete genome sequencing of three FmoPV strains showed genome sizes of 16,050 bases, the largest among morbilliviruses, because of unusually long 5′ trailer sequences of 400 nt. FmoPV possesses identical gene contents (3′-N-P/V/C-M-F-H-L-5′) and is phylogenetically clustered with other morbilliviruses. IgG against FmoPV N protein was positive in 49 sera (76.7%) of 56 RT-PCR–positive cats, but 78 (19.4%) of 401 RT-PCR–negative cats (
P
< 0.0001) by Western blot. FmoPV was isolated from CRFK feline kidney cells, causing cytopathic effects with cell rounding, detachment, lysis, and syncytia formation. FmoPV could also replicate in subsequent passages in primate Vero E6 cells. Infected cell lines exhibited finely granular and diffuse cytoplasmic fluorescence on immunostaining for FmoPV N protein. Electron microscopy showed enveloped virus with typical “herringbone” appearance of helical N in paramyxoviruses. Histological examination of necropsy tissues in two FmoPV-positive cats revealed interstitial inflammatory infiltrate and tubular degeneration/necrosis in kidneys, with decreased cauxin expression in degenerated tubular epithelial cells, compatible with tubulointerstitial nephritis (TIN). Immunohistochemical staining revealed FmoPV N protein-positive renal tubular cells and mononuclear cells in lymph nodes. A case-control study showed the presence of TIN in seven of 12 cats with FmoPV infection, but only two of 15 cats without FmoPV infection (
P
< 0.05), suggesting an association between FmoPV and TIN.
Structure-based ligand discovery for the protein–protein interface of chemokine receptor CXCR4
Authors: Mysinger Michael M. , Weiss Dahlia R. , Ziarek Joshua J. , Gravel Stéphanie , Doak Allison K. , Karpiak Joel , Heveker Nikolaus , Shoichet Brian K. , Volkman Brian F.
Published: March 2012

G-protein–coupled receptors (GPCRs) are key signaling molecules and are intensely studied. Whereas GPCRs recognizing small-molecules have been successfully targeted for drug discovery, protein-recognizing GPCRs, such as the chemokine receptors, claim few drugs or even useful small molecule reagents. This reflects both the difficulties that attend protein–protein interface inhibitor discovery, and the lack of structures for these targets. Imminent structure determination of chemokine receptor CXCR4 motivated docking screens for new ligands against a homology model and subsequently the crystal structure. More than 3 million molecules were docked against the model and then against the crystal structure; 24 and 23 high-scoring compounds from the respective screens were tested experimentally. Docking against the model yielded only one antagonist, which resembled known ligands and lacked specificity, whereas the crystal structure docking yielded four that were dissimilar to previously known scaffolds and apparently specific. Intriguingly, several were potent and relatively small, with IC
50
values as low as 306 nM, ligand efficiencies as high as 0.36, and with efficacy in cellular chemotaxis. The potency and efficiency of these molecules has few precedents among protein–protein interface inhibitors, and supports structure-based efforts to discover leads for chemokine GPCRs.
Distinct B-cell lineage commitment distinguishes adult bone marrow hematopoietic stem cells
Authors: Ghosn Eliver Eid Bou , Yamamoto Ryo , Hamanaka Sanae , Yang Yang , Herzenberg Leonard A. , Nakauchi Hiromitsu , Herzenberg Leonore A.
Published: March 2012

The question of whether a single hematopoietic stem cell (HSC) gives rise to all of the B-cell subsets [B-1a, B-1b, B-2, and marginal zone (MZ) B cells] in the mouse has been discussed for many years without resolution. Studies here finally demonstrate that individual HSCs sorted from adult bone marrow and transferred to lethally irradiated recipients clearly give rise to B-2, MZ B, and B-1b, but does not detectably reconstitute B-1a cells. These findings place B-2, MZ, and B-1b in a single adult developmental lineage and place B-1a in a separate lineage derived from HSCs that are rare or missing in adults. We discuss these findings with respect to known developmental heterogeneity in other HSC-derived lymphoid, myeloid, and erythroid lineages, and how HSC developmental heterogeneity conforms to the layered model of the evolution of the immune system that we proposed some years ago. In addition, of importance to contemporary medicine, we consider the implications that HSC developmental heterogeneity may have for selecting HSC sources for human transplantation.
Precision and Accuracy of Estimators of the Proportion of Hatchery‐Origin Spawners
Authors: Hinrichsen Richard A. , Sharma Rishi , Fisher Timothy R.
Published: March 2012

For salmon populations in the Columbia River basin, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimation of the proportion of hatchery‐origin spawners in spawning areas (p) is needed to make inferences about their status and potential for interbreeding with wild‐origin adults, which may reduce the genetic fitness of subsequent generations. Despite its importance, accurate and precise techniques for estimating p are lacking, especially when there are spawner inputs from multiple hatcheries in a single spawning area. To identify hatchery‐origin spawners, some hatchery releases are given visible marks, some are tagged with coded wire tags (CWTs), and some are marked in both ways. However, different marking fractions are used at different hatcheries and this complicates the problem of estimating p. To handle this situation, we derived a new generalized least‐squares estimator (GLSE) of p and another, less computationally intensive estimator that uses CWT recoveries alone (SMME). We conducted Monte Carlo simulations using both estimators to compare their precision and statistical accuracy. We then applied the estimators to 2010 carcass survey data for fall Chinook salmon Oncorhynchus tshawytscha in the Hanford Reach of the Columbia River. An incremental change away from identical marking fractions for all source hatchery releases reduced precision, increased bias, and complicated estimation. The GLSE had greater precision than the SMME. Statistical bias shrank as the true spawning population size, the fraction of hatchery‐origin fish, or the CWT fraction increased. The GLSE estimate of p in the Hanford Reach was 0.077, while the SMME estimate was 0.041. To maximize the accuracy and precision of the estimates of p, we recommend that identical marking fractions (preferably 100%) be used for all hatchery releases; barring this, we recommend that the CWT fractions be as large as possible.
Impacts of the Siberian High and Arctic Oscillation on the East Asia winter monsoon: Driving downwelling in the western Bering Sea
Authors: Wang Jia , Bai Xuezhi , Wang Dongxiao , Wang Daoru , Hu Haoguo , Yang Xiaoyi
Published: March 2012

The relationships between the wind fields of the East Asia winter monsoon (EAWM), the Siberian High (SH), and the Arctic Oscillation (AO) were investigated using reanalysis products. The winter anomalies of the wind fields were systematically examined from the Bering Sea, the Sea of Okhotsk (SoO), the Sea of Japan (SOJ), the East China Sea (ECS), and all the way to the South China Sea (SCS). The sea-level pressure (SLP) difference between the SH and the Aleutian Low (AL) determines the intensity of the EAWM.Wind field anomalies are controlled directly by the SH and indirectly by the AO that has significant impacts on the SH and AL. It is found that +SH enhances the EAWM, while +AO reduces the intensity of the EAWM by reducing the SLP difference (gradient) between the SH and AL; vice versa for the –SH and –AO, respectively. The surface air temperature (SAT) anomalies caused by the +SH result in a significant cooling in the downstream regions and a warming in the upstream regions; vice versa for the negative phase of the SH. The +AO produces a large warming in northern Eurasian and a cooling in the Bering Sea. Furthermore, using a Coupled Ice-Ocean Model (CIOM), it is found that the EAWM can produce a downwelling and dense water formation along the Siberian coast in the western Bering Sea, and also a significant surface-to-bottom convection over the Bering shelf, forming the winter shelf water, which can survive the summer as the so-called cold pool. The cold pool in the Bering Sea has significant impacts on marine ecosystems and habitat including fisheries, which has much implication to other marginal seas of East Asia.
The implications of El Niño-Southern Oscillation signal for South China monsoon climate
Authors: Zhou Wen , Chen Wen , Wang Dong Xiao
Published: March 2012

The objective of this research is to explore the impacts of El Niño-Southern Oscillation (ENSO) on a possible connection between winter monsoon and summer monsoon over South China. In boreal winter, the strong or weak northerly anomalies due to the East Asian winter monsoon (EAWM), sweep across the continent to the costal regions, which might be favorable for the occurrence of an ENSO event. In boreal summer, South China tends to experience less (more) rainfall and more (less) temperature extremes which might be in the mature phase of a warm (cold) ENSO event. It is also found that more frequent cold surges might be followed by less temperature extremes in the coming year. The possible connection might be that the western Pacific subtropical high after a strong (weak) EAWM year would move northward (southward) through the modification of a ENSO event; this northward (southward) western Pacific subtropical high might result in earlier (later) south China summer monsoon onset and lead to a strong (weak) summer monsoon in the coming year.
Seasonal variability of chlorophyll a fronts in the Luzon Strait based on satellite observations
Authors: Qiu Chunhua , Wang Dongxiao , He Zhigang , Chen Chuqun
Published: March 2012

Fronts are important sources of variability in the South China Sea basin, and they play significant roles in controlling bio-physical interactions in the Luzon Strait. We evaluated seasonality of chlorophyll a (chl-a) fronts in the Luzon Strait (LS) based on satellite observations from September 1997 to October 2007. Monthly-mean chl-a concentration at the front was highest in winter (0.8 mg m−3) and lowest in summer (0.3 mg m−3). Additionally, both the probability of frontal occurrence and the seasonal cycle of the gradient between offshore and nearshore chl-a showed that the chl-a front in the LS was the strongest in winter and weakest in summer. Pseudo wind stress played the most important role in shaping the spatial distribution of chl-a concentration, indicating that wind-driven upwelling is the mechanism involved.
Chemically modified multilayer graphene with metal interlayer as an efficient current spreading electrode for InGaN/GaN blue light-emitting diodes
Authors: Chandramohan S , Kang Ji Hye , Katharria Y S , Han Nam , Beak Yun Seon , Ko Kang Bok , Park Jong Bae , Ryu Beo Deul , Kim Hyun Kyu , Suh Eun-Kyung , Hong Chang-Hee
Published: March 2012

This paper describes a detailed systematic study based on the fabrication and performance of InGaN/GaN blue light-emitting diodes (LEDs) with multilayer graphene film as a current spreading electrode. Two facile approaches to improve the electrical coupling between graphene and p-GaN layer are demonstrated. Using chemical charge transfer doping, the work function (Φ) of graphene is tuned over a wide range from 4.21 to 4.93 eV with substantial improvements in sheet resistance (R
s). Compared with pristine graphene, the chemically modified graphene on p-GaN yields several appealing characteristics such as low specific contact resistance (ρc) and minimized barrier height. In addition, insertion of a thin gold interlayer between graphene and p-GaN profoundly enhances the contact properties at the interface. Combining these two approaches in a single LED, the current spreading and thus the device forward voltage (V
f) are considerably improved comparable to that of an LED fabricated with an indium tin oxide electrode. The importance of pre-metal deposition oxygen plasma treatment and rapid thermal annealing in improving the contact characteristics is also addressed.
Estimating Market Power of U.S. Dairy Cooperatives in the Fluid Milk Market
Authors: Cakir Metin , Balagtas Joseph V.
Published: March 2012

A structural econometric model of vertical relationships is adopted to identify pricing behavior in the supply chain for fluid milk in the United States. The model consists of a system of equations that allows estimation of oligopoly power of dairy co‐operatives and downstream firms, exploiting federal milk marketing order regulations to identify co‐operatives’ marginal cost. A key finding is that co‐operatives use their market power to raise the farm price of milk by almost 9% above marginal cost, resulting in an income transfer of more than $600 million per year in markets regulated by federal milk marketing orders.
Modeling A Household's Choice among Food Store Types
Authors: Dong Diansheng , Stewart Hayden
Published: March 2012

A household's choice among the different types of food stores to patronize depends on characteristics of both the stores and the household. Store characteristics include prices and promotional deals. Two types of household characteristics are important: the household's specific purchase history and demographics. This study proposes a new multinomial logit model to account for these choice determinants. In an empirical application to fluid milk, we find that store characteristics and both household demographics and purchase history are significant determinants of a household's store‐type choices and must all be included in a choice model.
Kwoniella shandongensis sp. nov., a basidiomycetous yeast isolated from soil and bark from an apple orchard
Authors: Chen Ru , Jiang Yuan-Mao , Wei Shao-Chong , Wang Qi-Ming
Published: March 2012

Four basidiomycetous yeast strains (Y13-1T, Y2-1, Y6-3 and Y8-2) were isolated from soil and bark collected from an apple orchard in Tai’an, Shandong province, PR China. Phylogenetic analysis based on 26S rRNA gene D1/D2 domains and ITS regions revealed that these novel strains were located in the Kwoniella clade in the class Tremellomycetes and were closely related to Cryptococcus cuniculi and Kwoniella heveanensis, but were clearly distinct from these species. Therefore, it is proposed that the new strains represent a novel species, Kwoniella shandongensis sp. nov., with the type strain Y13-1T( = CGMCC 2.04458T = CBS 12478T). The MycoBank number for the novel species is MB 564868.
Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata
Authors: Tsukahara Sayuri , Kawabe Akira , Kobayashi Akie , Ito Tasuku , Aizu Tomoyuki , Shin-i Tadasu , Toyoda Atsushi , Fujiyama Asao , Tarutani Yoshiaki , Kakutani Tetsuji
Published: March 2012

The plant genome evolves with rapid proliferation of LTR-type retrotransposons, which is associated with their clustered accumulation in gene-poor regions, such as centromeres. Despite their major role for plant genome evolution, no mobile LTR element with targeted integration into gene-poor regions has been identified in plants. Here, we report such targeted integrations de novo. We and others have previously shown that an ATCOPIA93 family retrotransposon in Arabidopsis thaliana is mobilized when the DNA methylation machinery is compromised. Although ATCOPIA93 family elements are low copy number in the wild-type A. thaliana genome, high-copy-number related elements are found in the wild-type Arabidopsis lyrata genome, and they show centromere-specific localization. To understand the mechanisms for the clustered accumulation of the A. lyrata elements directly, we introduced one of them, named Tal1 (Transposon of Arabidopsis lyrata 1), into A. thaliana by transformation. The introduced Tal1 was retrotransposed in A. thaliana, and most of the retrotransposed copies were found in centromeric repeats of A. thaliana, suggesting targeted integration. The targeted integration is especially surprising because the centromeric repeat sequences differ considerably between A. lyrata and A. thaliana. Our results revealed unexpectedly dynamic controls for evolution of the transposon-rich heterochromatic regions.
Embryonic onset of late replication requires Cdc25 down-regulation
Authors: Farrell Jeffrey A. , Shermoen Antony W. , Yuan Kai , O'Farrell Patrick H.
Published: March 2012

The Drosophila midblastula transition (MBT), a major event in embryogenesis, remodels and slows the cell cycle. In the pre-MBT cycles, all genomic regions replicate simultaneously in rapid S phases that alternate with mitosis, skipping gap phases. At the MBT, down-regulation of Cdc25 phosphatase and the resulting inhibitory phosphorylation of the mitotic kinase Cdk1 create a G2 pause in interphase 14. However, an earlier change in interphase 14 is the prolongation of S phase. While the signals modifying S phase are unknown, the onset of late replication—where replication of constitutively heterochromatic satellite sequences is delayed—extends S-phase 14. We injected Cdc25 mRNA to bypass the developmentally programmed down-regulation of Cdc25 at the MBT. Introduction of either Cdc25 isoform (String or Twine) or enhanced Cdk1 activity triggered premature replication of late-replicating sequences, even after their specification, and thereby shortened S phase. Reciprocally, reduction of Cdk1 activity by knockdown of mitotic cyclins extended pre-MBT S phase. These findings suggest that high Cdc25 and Cdk1 contribute to the speed of the rapid, pre-MBT S phases and that down-regulation of these activities plays a broader role in MBT-associated changes than was previously suspected.
Cross‐functional integration and performance: what are the real benefits?
Authors: Turkulainen Virpi , Ketokivi Mikko
Published: March 2012

Purpose

Conventional wisdom has it that cross‐functional integration is a “must”. The purpose of this paper is to take an information‐processing approach to integration and elaborate the conventional wisdom by theoretical examination of both the concept of integration as well as theoretical and empirical elaboration of its link to operational performance.

Design/methodology/approach

The authors develop six propositions on how cross‐functional integration affects performance and test the propositions in an international sample of 266 manufacturing plant organizations in nine countries.

Findings

The results strongly suggest that disaggregation of performance is important, because the effects of cross‐functional integration on performance are contingent: even though the effects of achieved integration on several dimensions of operational performance are positive, the performance effect varies from one dimension to the next. This is an important finding given that performance has typically been treated at an aggregate level in prior research on the performance effects of integration.

Originality/value

Although most research on integration has focused on the performance implications in particular, theoretical work on the nature of the integration‐performance relationship is required. In this paper, the authors argue the benefits of cross‐functional integration to be fundamentally context‐dependent and elaborate the link between integration and performance by developing the definition of the concept of integration further, as well as by disaggregation of performance, to its constituent dimensions.