bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing internal stress evolution in unsaturated soils
Authors: Abou Najm Majdi , Mohtar Rabi H. , Weiss Jason , Braudeau Erik
Published: January 2009

Internal stresses in soils evolve as a result of the various interactions among soil particles and the pore fluids in response to natural or human‐induced activities. Whether attributed to suction, structure, or the various physicochemical forces that may develop, assessing the internal stresses in soils has been an active area of research in soil science and engineering. This paper presents the restrained ring method as an experimental tool for measuring the stresses that develop in a drying soil when it is restrained from shrinking freely. The internal stress that develops can be related to the water content of the soil. This method is validated using results for both silty clay loam and clay loam soils. Tensile stress at failure (estimated from the restrained ring method) was compared to tensile strength ranges of similar soils, and a good correlation was observed. Moreover, internal stresses measured by the restrained ring method were compared with existing empirical relationships (using suction and degree of saturation). This comparison concluded that suction is not the sole contributor to the soil's internal stress.
Calibration‐constrained Monte Carlo analysis of highly parameterized models using subspace techniques
Authors: Tonkin Matthew , Doherty John
Published: January 2009

We describe a subspace Monte Carlo (SSMC) technique that reduces the burden of calibration‐constrained Monte Carlo when undertaken with highly parameterized models. When Monte Carlo methods are used to evaluate the uncertainty in model outputs, ensuring that parameter realizations reproduce the calibration data requires many model runs to condition each realization. In the new SSMC approach, the model is first calibrated using a subspace regularization method, ideally the hybrid Tikhonov‐TSVD “superparameter” approach described by Tonkin and Doherty (2005). Sensitivities calculated with the calibrated model are used to define the calibration null‐space, which is spanned by parameter combinations that have no effect on simulated equivalents to available observations. Next, a stochastic parameter generator is used to produce parameter realizations, and for each a difference is formed between the stochastic parameters and the calibrated parameters. This difference is projected onto the calibration null‐space and added to the calibrated parameters. If the model is no longer calibrated, parameter combinations that span the calibration solution space are reestimated while retaining the null‐space projected parameter differences as additive values. The recalibration can often be undertaken using existing sensitivities, so that conditioning requires only a small number of model runs. Using synthetic and real‐world model applications we demonstrate that the SSMC approach is general (it is not limited to any particular model or any particular parameterization scheme) and that it can rapidly produce a large number of conditioned parameter sets.
Charge states of energetic ions in Jupiter's radiation belt inferred from absorption microsignatures of Io
Authors: Selesnick R. S. , Cohen C. M. S.
Published: January 2009

The Heavy Ion Counter on the Galileo Jupiter orbiter observed depletions of energetic (≳5 MeV/nucleon) oxygen and sulfur ions near Io that are interpreted as absorption microsignatures. The two elements were equally abundant in this region of Jupiter's radiation belt. Numerical simulations of microsignatures from Galileo orbits 27, 31, and 32, based on calculations of ion trajectories in models of the magnetospheric and Alfvén wing magnetic fields, show that the data are most consistent with the ions being fully ionized or nearly so. The conclusion is independent of field model inaccuracies, which cause some discrepancy between simulations and data, because the Alfvén wing field significantly deflects only those trajectories with relatively small gyroradii.
Sea level extremes in southern Europe
Authors: Marcos Marta , Tsimplis Michael N. , Shaw Andrew G. P.
Published: January 2009

Knowledge of sea level extremes is important for coastal planning purposes. Temporal changes in the extremes may indicate changes in the forcing parameters, most probably the storm surges. Sea level extremes and their spatial and temporal variability in southern Europe are explored on the basis of 73 tide gauge records from 1940. This study uses all data available to infer risks at the coast caused by extreme sea levels. Extreme values of 250 cm are observed at the Atlantic coasts with smaller values in the Mediterranean where, with the exception of the Strait of Gibraltar and the Adriatic Sea, the extreme values are less than 60 cm. At the Adriatic Sea values of up to 200 cm are found. When the tidal contribution is removed the differences between the various areas reduce. The spatial distribution of the extremes of the tidal residuals is well represented by the hindcast of a two‐dimensional hydrodynamic model forced by the atmospheric pressure and the wind, although the model underestimates the extremes. Higher return levels (200–300 cm for the 50‐year return level) are observed in the Atlantic stations due to the larger tides. In the Mediterranean, higher values are found in the northern Adriatic (between 150 and 200 cm) while in the rest of the domain they vary between 20 and 60 cm. The nonlinear interaction between tides and surges is negligible in the Mediterranean, thus the joint tides‐surges distribution can be applied. The interannual and decadal variability in time of extremes is caused by mean sea level changes.
Validation of Moderate Resolution Imaging Spectroradiometer (MODIS) albedo retrieval algorithm: Dependence of albedo on solar zenith angle
Authors: Liu Jicheng , Schaaf Crystal , Strahler Alan , Jiao Ziti , Shuai Yanmin , Zhang Qingling , Roman Miguel , Augustine John A. , Dutton Ellsworth G.
Published: January 2009

The Moderate Resolution Imaging Spectroradiometer (MODIS) bidirectional reflectance distribution function (BRDF)/albedo algorithm uses multiday, multiband MODIS surface reflectance products from Terra and Aqua to produce a global albedo product at a 500 m resolution (Collection 5). This paper evaluates the ability of the MODIS albedo product to represent albedos at all diurnal solar zenith angles through a comparison with field measurements from the Surface Radiation Budget Network (SURFRAD) and the Atmospheric Radiation Measurement Southern Great Plains (ARM/SGP) stations. The results show that, for most of the sites, the overall accuracy of the MODIS albedo is within 0.05 and shows an increasing negative bias and increased RMSE as zenith angle increases beyond 70°–75° as compared to the ground observations. The full inversion of the MODIS BRDF/albedo algorithm has a higher inversion quality than the backup algorithm. Site heterogeneity and spatial‐scale mismatch between the MODIS and ground observations are the major factors contributing to the discrepancy between the MODIS albedo and the field measurements.
Effects of soil wetness, plant litter, and under‐canopy atmospheric stability on ground evaporation in the Community Land Model (CLM3.5)
Authors: Sakaguchi Koichi , Zeng Xubin
Published: January 2009

The National Center for Atmospheric Research (NCAR) Community Land Model Version 3.5 (CLM3.5) has significantly improved the simulation of hydrologic cycles compared to its earlier version (CLM3.0) owing to a series of new and modified parameterizations for canopy and soil processes. One of the key elements is the addition of a soil resistance to effectively reduce soil evaporation (Es) and improve the partitioning of evapotranspiration. This soil resistance, however, is found to be physically inconsistent under wet soil conditions and implicitly include the effects of dead leaves. A new treatment with three components are proposed here: (1) two different approaches to better reflect the soil moisture limitation to Es, the so‐called α and β methods combined and a new soil resistance; (2) a new surface resistance to explicitly represent the effect of plant litter cover on water vapor transfer; and (3) an explicit consideration of the effect of under‐canopy atmospheric stability on the under‐canopy turbulent resistance. The effects of each modification vary locally and seasonally, and their combination leads to regional differences between CLM3.5 and our new formulations. Our new formulations tend to have higher Es over high latitudes and similar or slightly higher Es in dry regions. A larger reduction of Es by the new formulations is also found over regions with relatively wet soil and more vegetation, in better agreement with previous ET partitioning studies.
Defective Neuropeptide Processing and Ischemic Brain Injury: A Study on Proprotein Convertase 2 and its Substrate Neuropeptide in Ischemic Brains
Authors: Zhan Shuqin , Zhao Hongbo , White Aaron J , Minami Manabu , Pignataro Giuseppe , Yang Tao , Zhu Xiaorong , Lan Jingquan , Xiong Zhigang , Steiner Donald F , Simon Roger P , Zhou An
Published: January 2009

Using a focal cerebral ischemia model in rats, brain ischemia-induced changes in expression levels of mRNA and protein, and activities of proprotein convertase 2 (PC2) in the cortex were examined. In situ hybridization analyses revealed a transient upregulation of the mRNA level for PC2 at an early reperfusion hour, at which the level of PC2 protein was also high as determined by immunocytochemistry and western blotting. When enzymatic activities of PC2 were analyzed using a synthetic substrate, a significant decrease was observed at early reperfusion hours at which levels of PC2 protein were still high. Also decreased at these reperfusion hours were tissue levels of dynorphin-A(1-8) (DYN-A(1-8)), a PC2 substrate, as determined by radioimmunoassay. Further examination of PC2 protein biosynthesis by metabolic labeling in cultured neuronal cells showed that in ischemic cells, the proteolytic processing of PC2 was greatly attenuated. Finally, in mice, an intracerebroventricular administration of synthetic DYN-A(1-8) significantly reduced the extent of ischemic brain injury. In mice those lack an active PC2, exacerbated brain injury was observed after an otherwise non-lethal focal ischemia. We conclude that brain ischemia attenuates PC2 and PC2-mediated neuropeptide processing. This attenuation may play a role in the pathology of ischemic brain injury.
Cooling Combined with Immediate or Delayed Xenon Inhalation Provides Equivalent Long-Term Neuroprotection after Neonatal Hypoxia—Ischemia
Authors: Thoresen Marianne , Hobbs Catherine E , Wood Tommy , Chakkarapani Ela , Dingley John
Published: January 2009

Hypothermia (HT) improves outcome after neonatal hypoxia–ischemia. Combination therapy may extend neuroprotection. The noble anesthetic gas xenon (Xe) has an excellent safety profile. We have shown earlier that 3 h of 50% Xe plus HT (32°C) additively gives more protection (72%) than either alone (HT = 31.1%, Xe = 10.2%). Factors limiting clinical use include high-cost and specialist administration requirements. Thus, combinations of 1 h of 50% Xe were administered concurrently for either the first (1 hImmediateXe) or last (1 hDelayedXe) of 3 h of posthypoxic–ischemic HT as compared with 3 h of 50% Xe/HT to investigate how brief Xe exposure with a delay would affect efficacy. An established neonatal rat hypoxia–ischemia model was used. Serial functional neurologic testing into adulthood was performed, followed by neuropathological examination. Xenon with HT was more effective with longer Xe duration (3 h versus 1 h) ( P = 0.015). However, 1 h Xe/3 h HT resulted in better neuroprotection than 3 h HT alone ( P = 0.03), this significant effect was also present with 1 h Xe after a 2-h delay. One (immediate or with a delay) or 3 h Xe also significantly improved motor function ( P= 0.024). Females had significantly better motor scores than males, but no sex-dependent difference in pathology results. The neuroprotection of short, delayed Xe treatment would allow transport to specialist facilities to receive Xe.
Tetrapyrrole signal as a cell-cycle coordinator from organelle to nuclear DNA replication in plant cells
Authors: Kobayashi Yuki , Kanesaki Yu , Tanaka Ayumi , Kuroiwa Haruko , Kuroiwa Tsuneyoshi , Tanaka Kan
Published: January 2009

Eukaryotic cells arose from an ancient endosymbiotic association of prokaryotes, with plant cells harboring 3 genomes as the remnants of such evolution. In plant cells, plastid and mitochondrial DNA replication [organelle DNA replication (ODR)] occurs in advance of the subsequent cell cycles composed of nuclear DNA replication (NDR) and cell division. However, the mechanism by which replication of these genomes with different origins is coordinated is largely unknown. Here, we show that NDR is regulated by a tetrapyrrole signal in plant cells, which has been suggested as an organelle-to-nucleus retrograde signal. In synchronized cultures of the primitive red alga
Cyanidioschyzon merolae
, specific inhibition of A-type cyclin-dependent kinase (CDKA) prevented NDR but not ODR after onset of the cell cycle. In contrast, inhibition of ODR by nalidixic acid also resulted in inhibition of NDR, indicating a strict dependence of NDR on ODR. The requirement of ODR for NDR was bypassed by addition of the tetrapyrrole intermediates protoporphyrin IX (ProtoIX) or Mg-ProtoIX, both of which activated CDKA without inducing ODR. This scheme was also observed in cultured tobacco cells (BY-2), where inhibition of ODR by nalidixic acid prevented CDKA activation and NDR, and these inhibitions were circumvented by Mg-ProtoIX without inducing ODR. We thus show that tetrapyrrole-mediated organelle–nucleus replicational coupling is an evolutionary conserved process among plant cells.
The CD5 ectodomain interacts with conserved fungal cell wall components and protects from zymosan-induced septic shock-like syndrome
Authors: Vera Jorge , Fenutría Rafael , Cañadas Olga , Figueras Maite , Mota Rubén , Sarrias Maria-Rosa , Williams David L. , Casals Cristina , Yelamos José , Lozano Francisco
Published: January 2009

The CD5 lymphocyte surface receptor is a group B member of the ancient and highly conserved scavenger receptor cysteine-rich superfamily. CD5 is expressed on mature T and B1a cells, where it is known to modulate lymphocyte activation and/or differentiation processes. Recently, the interaction of a few group B SRCR members (CD6, Spα, and DMBT1) with conserved microbial structures has been reported. Protein binding assays presented herein indicate that the CD5 ectodomain binds to and aggregates fungal cells (Schizosaccharomyces pombe,Candida albicans, andCryptococcus neoformans) but not to Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus) bacteria. Accordingly, the CD5 ectodomain binds to zymosan but not to purified bacterial cell wall constituents (LPS, lipotheicoic acid, or peptidoglycan), and such binding is specifically competed by β-glucan but not by mannan. TheKdof the rshCD5/(1→3)-β-d-glucan phosphate interaction is 3.7 ± 0.2 nM as calculated from tryptophan fluorescence data analysis of free and bound rshCD5. Moreover, zymosan binds to membrane-bound CD5, and this induces both MAPK activation and cytokine release. In vivo validation of the fungal binding properties of the CD5 ectodomain is deduced from its protective effect in a mouse model of zymosan-induced septic shock-like syndrome. In conclusion, the present results indicate that the CD5 lymphocyte receptor may sense the presence of conserved fungal components [namely, (1→3)-β-d-glucans] and support the therapeutic potential of soluble CD5 forms in fungal sepsis.
The transition state for integral membrane protein folding
Authors: Curnow Paul , Booth Paula J.
Published: January 2009

Biology relies on the precise self-assembly of its molecular components. Generic principles of protein folding have emerged from extensive studies on small, water-soluble proteins, but it is unclear how these ideas are translated into more complex situations. In particular, the one-third of cellular proteins that reside in biological membranes will not fold like water-soluble proteins because membrane proteins need to expose, not hide, their hydrophobic surfaces. Here, we apply the powerful protein engineering method of Φ-value analysis to investigate the folding transition state of the alpha-helical membrane protein, bacteriorhodopsin, from a partially unfolded state. Our results imply that much of helix B of the seven-transmembrane helical protein is structured in the transition state with single-point alanine mutations in helix B giving Φ values >0.8. However, residues Y43 and T46 give lower Φ values of 0.3 and 0.5, respectively, suggesting a possible reduction in native structure in this region of the helix. Destabilizing mutations also increase the activation energy of folding, which is accompanied by an apparent movement of the transition state toward the partially unfolded state. This apparent transition state movement is most likely due to destabilization of the structured, unfolded state. These results contrast with the Hammond effect seen for several water-soluble proteins in which destabilizing mutations cause the transition state to move toward, and become closer in energy to, the folded state. We thus introduce a classic folding analysis method to membrane proteins, providing critical insight into the folding transition state.
The influence of maternal age on the outcomes of pregnancies complicated by bleeding at less than 12 weeks
Authors: MBUGUA GITAU GODFREY , LIVERSEDGE HELEN , GOFFEY DAWN , HAWTON ANNEMARIE , LIVERSEDGE NEIL , TAYLOR MYLES
Published: January 2009

The effect of maternal age on the outcome of threatened miscarriage after ultrasound has confirmed fetal heart (FH) pulsation was assessed. At a university teaching hospital, 138 women presenting with bleeding before 12 weeks’ gestation were followed up until delivery or pregnancy loss. Those with multiple or ectopic pregnancy, social termination of pregnancy, assisted conception and temporary residence were excluded. Outcome measures were pregnancy loss, fetal abnormalities, preterm delivery, low birthweight and cesarean delivery. Age over 35 years was significantly associated with reduced live‐birth and increased miscarriage rates. Women over 35 years of age had higher cesarean section and pregnancy loss rates than the younger women. The combination of bleeding in early pregnancy and advanced age increases risk of pregnancy loss even after ultrasound has confirmed FH pulsation.
Cesarean section is associated with more frequent pneumothorax and respiratory problems in the neonate
Authors: BENTERUD TORKIL , SANDVIK LEIV , LINDEMANN ROLF
Published: January 2009

We have investigated whether the incidence of neonatal pneumothorax (NP), use of mechanical ventilation (MV) or Continuous Positive Airways Pressure (CPAP) is increased in neonates delivered at term and preterm by cesarean section (CS). All deliveries at Ullevål University Hospital, Oslo, during the period 2001–2005 (n = 29,358) were included, among whom 5,957 were delivered by CS (20.3%). Data were collected on mode of delivery, elective or emergency CS, gestational age, maternal age, gender and parity. Among the 26,664 neonates born at term (≥37th gestational week), 4,546 were delivered by CS (17.0%), of whom 0.5% by elective and 0.6% by emergency CS with NP. The incidence of diagnosed NP was significantly higher after CS than after vaginal delivery (0.6% vs. 0.10%, p<0.001). In addition, the need for MV was significantly increased (0.41% vs. 0.19%; p = 0.01) but use of CPAP was not (0.28%vs. 0.15%; p = 0.08). Among 2,694 neonates born preterm (<37th gestational week), 1,266 were delivered by CS (47.0%). The incidence of diagnosed NP was 2.05% when delivered by CS but only 0.63% when delivered vaginally (p<0.01). Among the preterm infants delivered by CS, 17.7% needed CPAP compared to 6.9% when delivered vaginally (p<0.001) and MV was required for 8.1 and 3.7% (p<0.001), respectively. Among neonates delivered at term or moderately preterm (30–36 weeks) by CS the incidence of NP and other respiratory problems was significantly increased.
Urethrography in the male: The clamp method
Authors: Berná J. D. , Berná J. D. , Meson M. Aparicio
Published: January 2009

Background: Retrograde urethrography is considered the gold standard for evaluating stenosis or urethral disease.

Purpose: To describe the clamp method for optimizing retrograde urethrography (RUG) using a perfected device and a drip infusion system.

Material andMethods: RUG was performed in 42 patients with a mean age of 63.4±16.5 years suspected of having urethral stenosis. The modifications to the device are shown, and the steps of the technique described. The intensity of pain from both catheterization and external compression was measured on a visual analog scale (VAS).

Results: All the RUG examinations were conducted satisfactorily. The use of the drip infusion system enabled visualization of the posterior urethra in 97.6% of cases, and bladder repletion was achieved in 95.2% of cases. The urethrograms revealed images of stenosis in 31 patients. With catheterization the mean pain intensity registered by VAS was 0.7±0.6 (SD), whereas with external compression the mean pain intensity was 0.06±0.02 (SD).

Conclusion: The clamp method and drip infusion system used in this study are efficient and reduce patient discomfort. The procedure makes it possible to assess cases with stenosis close to the meatus that are difficult to manage with the conventional method.
Fossa trochanterica of the proximal femur in rabbits: An anatomic structure for potential misinterpretation on magnetic resonance images
Authors: Wang Hao-Hao , Wang Yi-Xiang J. , Sheng Hui , Zhang Ge , Qin Ling , Ahuja Anil T. , Teng Li-Song
Published: January 2009

Background: Magnetic resonance imaging (MRI) has been increasingly used as an investigational tool for assessing the structure and function of animal skeletal disease models. However, to date, MRI tomographic knowledge of laboratory animal skeletal anatomy and pathology remains limited.

Purpose: To demonstrate that fossa trochanterica of the proximal femur in rabbits can potentially be misinterpreted as a bone lesion on MR images.

Material and Methods: Twenty 28–30-week-old male New Zealand white rabbits were used in the study. Corticosteroid-induced osteonecrosis induction was carried out with a combined administration of lipopolysaccharide and methylprednisolone. In this animal model, it is known that osteonecrosis commonly occurs in the proximal femur. MRI at 1.5T was performed before osteonecrosis induction, and at 1 and 2 weeks post-osteonecrosis induction. For anatomical imaging of the proximal femur, coronal sectional images were obtained to align the femoral head, neck, and proximal shaft in a single plane. Volumetric computed tomography (CT) comprised continuous axial acquisitions through the bilateral hip joints and femurs and was performed on one age- and sex-matched New Zealand white rabbit to correlate MRI anatomical findings.

Results: In 30% of the acquired normal data sets, a low-signal area surrounded by high-signal bone marrow was observed slightly distal to the femoral head and medial to the third trochanter. This dark, low-signal area resembled an osteonecrosis lesion on MR images. Volumetric CT clarified that the low MR signal was due to the deep fossa trochanterica structure in the rabbit proximal femur.

Conclusion: Improved understanding of the cross-sectional anatomy of the fossa trochanterica in the rabbit proximal femur will prevent misinterpretation as a bone lesion on MR images.
TOWARDS A EUROPEAN SOCIAL MODEL?
Authors: Montanari Ingalill , Nelson Kenneth , Palme Joakim
Published: January 2009

The market-enhancing regulations of the European Union (EU) place political and economic constraints on the Member States. This has been expected to induce convergence of social policies, generally in a downward direction. At the same time the notion of a European Social Model has been launched as a strategy to make marketization socially acceptable, pointing to a development in a different direction. This paper examines key aspects of the development of the main social insurance programs during the period 1980–2000 in 14 EU Member States. Are there significant signs of convergence in the replacement rates of social insurance programs and do broader development trends of the social insurance systems indicate converging institutional models? The results indicate divergence rather than convergence of social insurance replacement rates. In terms of institutional models there is no evidence of a common European Social Model in the area of social insurance over the past decades.
FIRST-TIME JOBSEEKERS VERSUS UNEMPLOYED WITH PREVIOUS WORK EXPERIENCE
Authors: Covizzi Ilaria
Published: January 2009

Italy has one of the highest incidences of long-term unemployment among OECD countries. The share of first-time jobseekers among the long-term unemployed is outstanding compared to that of the unemployed who have lost a job. Using data from the Italian Household Panel survey and event history analysis, this paper investigates the impact of individual, familial and institutional factors on the duration of unemployment spells of Italian first-time jobseekers and those unemployed who have lost their job, and assesses the issue of duration dependence. Findings emphasise the importance from a policy perspective of analysing these two unemployment experiences separately. The two unemployed groups undergo very different processes of exiting unemployment due to some specific institutional and structural features of the Italian socio-economic context. Results indicate that in Italy the chances of finding a first job decrease with time, and education proves to be effective only after long job searches. On the contrary, among Italian adult unemployed the probability of finding a new job largely depends on individual and familial characteristics rather than on mechanisms associated to the length of time spent unemployed.
UNIVERSAL DISADVANTAGE?
Authors: Warren Tracey
Published: January 2009

Working fewer than full-time hours has been seen as a crucial way in which women workers can balance demands from home and paid work. But working part-time holds a range of negative repercussions for other aspects of worker's lives, in particular their economic well-being. Examining objective and subjective indicators of economic well-being, the paper uses data from the European Community Household Panel Survey to consider the ramifications of working short hours for women in Europe. The paper is concerned with the generalisability of the very weak situation of part-timers in Britain. It asks whether and how the economic problems faced by women at the bottom of the occupational hierarchy differ according to societal context. The papers shows that part-time low level workers had the lowest monthly wages relative to their compatriots in each country examined, though the intensity of wage disadvantage varied substantially across the sample. The research did not uncover a universal positive correlation between women's relative wage positions and individual level measures of economic well-being, however. The most prevalent association between working part-time in a low level occupation and facing a weak economic position occurred at the level of household economies. The paper concludes by asking how we best research economic well-being, including whether it should be approached via an individual or household level analysis.
SURVEILLANCE IN GERMANY AFTER 9/11
Authors: Topal Çagatay
Published: January 2009

After the terrorist attacks on September 11, 2001, surveillance pressure on immigrants increased considerably. The trend was the globalization of surveillance of the world population but especially of immigrants. 9/11 was not a turning point, however, since surveillance was already headed towards being globalized. The post-9/11 context accelerated this process. The economic and political developments that have taken place after 9/11 demonstrate that the processes of globalization, immigration and surveillance are closely linked. Today, immigrants from Turkey in Germany experience surveillance within this context. The regulations of the European Union, the policies of the German government and global political-economic processes play interdependent roles in this surveillance which is now more intensified, focused, arbitrary and widespread. Those groups who are economically, religiously, politically, and culturally marginalized are the primary targets of surveillance. The case of immigrants from Turkey can be used to exemplify the surveillance of immigrants in advanced capitalist countries.
Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12Drosophilagenomes
Authors: Alvarez-Ponce David , Aguadé Montserrat , Rozas Julio
Published: January 2009

Biological function is based on complex networks consisting of large numbers of interacting molecules. The evolutionary properties of molecular networks and, in particular, the impact of network architecture on the sequence evolution of its individual components are, nonetheless, still poorly understood. Here, we conducted a fine-scale network-level molecular evolutionary analysis of the insulin/TOR pathway across 12 species ofDrosophila. We found that the insulin/TOR pathway components are completely conserved across these species and that two genes located at major network branch points show evidence for positive selection. Remarkably, we detected a gradient in the strength of purifying selection along the pathway, increasing from the upstream to the downstream genes. We also found that physically interacting proteins tend to have more similar levels of selective constraint, even though this feature might represent a byproduct of the correlation between selective constraint and the pathway position. Our results clearly indicate that the levels of functional constraint do depend on the position of the proteins in the pathway and, consequently, the architecture of the pathway constrains gene sequence evolution.
Epidermal Cell Death in Rice Is Confined to Cells with a Distinct Molecular Identity and Is Mediated by Ethylene and H2O2 through an Autoamplified Signal Pathway
Authors: Steffens Bianka , Sauter Margret
Published: January 2009

Rice (Oryza sativa) forms adventitious root primordia at stem nodes during normal development. Root emergence is preceded by ethylene-induced, H2O2-mediated local death of epidermal cells. Exogenous H2O2 or enhancement of endogenous H2O2 promoted epidermal cell death in a dose-dependent manner. Inhibition of NADPH oxidase lowered ethylene-induced cell death rates. Inhibition of ethylene perception by 1-methylcyclopropene did not abolish H2O2-induced cell death, indicating that H2O2 acts downstream of ethylene. Microarray studies of epidermal cells that undergo cell death identified 61 genes coregulated by the ethylene-releasing compound ethephon and by H2O2, supporting a joint signaling pathway. Regulation of the ethylene biosynthetic genes 1-Aminocyclopropane-1-Carboxylate Oxidase1 and Ethylene Overproducer-Like1 and downregulation of Metallothionein2b (MT2b), which encodes a reactive oxygen scavenger, indicated mutual enhancement of ethylene and H2O2 signaling. Analysis of MT2b knockdown mutants showed that cell death rates were inversely related to MT2b transcript abundance. Epidermal cells above adventitious roots have a morphological and molecular identity distinct from other epidermal cells. Pro-death signals regulated several transcription factor genes with a proposed function in cell type specification. It is hypothesized that induction of cell death is dependent on epidermal cell identity.
STARCH-EXCESS4 Is a Laforin-Like Phosphoglucan Phosphatase Required for Starch Degradation in Arabidopsis thaliana
Authors: Kötting Oliver , Santelia Diana , Edner Christoph , Eicke Simona , Marthaler Tina , Gentry Matthew S. , Comparot-Moss Sylviane , Chen Jychian , Smith Alison M. , Steup Martin , Ritte Gerhard , Zeeman Samuel C.
Published: January 2009

Starch is the major storage carbohydrate in plants. It is comprised of glucans that form semicrystalline granules. Glucan phosphorylation is a prerequisite for normal starch breakdown, but phosphoglucan metabolism is not understood. A putative protein phosphatase encoded at the Starch Excess 4 (SEX4) locus of Arabidopsis thaliana was recently shown to be required for normal starch breakdown. Here, we show that SEX4 is a phosphoglucan phosphatase in vivo and define its role within the starch degradation pathway. SEX4 dephosphorylates both the starch granule surface and soluble phosphoglucans in vitro, and sex4 null mutants accumulate phosphorylated intermediates of starch breakdown. These compounds are linear α-1,4-glucans esterified with one or two phosphate groups. They are released from starch granules by the glucan hydrolases α-amylase and isoamylase. In vitro experiments show that the rate of starch granule degradation is increased upon simultaneous phosphorylation and dephosphorylation of starch. We propose that glucan phosphorylating enzymes and phosphoglucan phosphatases work in synergy with glucan hydrolases to mediate efficient starch catabolism.
Polymorphism of K2Co2Mo3O12: variations in the packing schemes and changes in molybdenum coordination under high pressure
Authors: Engel J. M. , Ahsbahs H. , Fuess H. , Ehrenberg H.
Published: January 2009

Within systematic studies on the K–Co–Mo–O system so-called high-temperature and high-pressure modifications of K2Co2Mo3O12 were found. The Birch–Murnaghan fits for the ambient-conditions modification α (Z = 4) and the high-pressure phase II (Z = 8) lead to V
0 = 1193.09 (4) Å3, K = 30.8 (8) GPa, K_0^{\prime} = 5.4 (4) and V
0 = 2170 (10) Å3, K = 51 (2) GPa with K_0^{\prime} fixed at 4.0, respectively. The high-pressure phase transition is denoted as pseudoreconstructive [Wiesmann et al. (1997). J. Solid State Chem.
132, 88–97], because some [MoO4] tetrahedra turn into edge-sharing pairs of [MoO5] pyramids or face-sharing pairs of [MoO6] octahedra. The new phases are presented and compared with the α phase.
Crystallochemical formula as a tool for describing metal–ligand complexes – a pyridine-2,6-dicarboxylate example
Authors: Serezhkin Viktor N. , Vologzhanina Anna V. , Serezhkina Larisa B. , Smirnova Ekaterina S. , Grachova Elena V. , Ostrova Polina V. , Antipin Mikhail Yu.
Published: January 2009

Compounds (299) containing 494 symmetrically independent pyridine-2,6-dicarboxylate moieties have been investigated. Among them the structures of Na3[Nd(Pydc)3]·14H2O and Na3[Er(Pydc)3]·11.5H2O, where H2Pydc is pyridine-2,6-dicarboxylic acid, were determined by single-crystal X-ray diffraction, while the others were taken from the Cambridge Structural Database. The characteristics of any complex by means of the `method of crystallochemical analysis' are described, and the coordination types of all the Pydc ions and crystallochemical formulae of all the compounds were determined. Although the ion can act as a mono-, bi-, tri-, tetra- and pentadentate ligand, 96% of Pydc ions are coordinated to the central A atom in the tridentate-chelating mode. The dependence of the denticity and geometry of pyridine-2,6-dicarboxylate, as well as of the composition of Pydc-containing complexes, was studied as a function of the nature of the A atom, the molar ratio Pydc:A and the presence of neutral or acidic ligands in the reaction mixture.
Probing the shapes of chiral bis-(o-naphthalimidobenzoyl) systems using X-ray and circular dichroism methods
Authors: Rychlewska Urszula , Plutecka Agnieszka , Hoffmann Marcin , Skowronek Paweł , Gawrońska Krystyna , Gawroński Jacek
Published: January 2009

CD (circular dichroism) and X-ray investigations have been carried out in order to identify the prevalent conformations and define the forces that determine the molecular and supramolecular organization of the alkyl-bridged bichromophoric [NAB, ortho-(1,8-naphthalimido)benzoyl] units, each consisting of the benzoyl substituted in the ortho position with the 1,8-naphthalimide group. The results reveal that NAB bichromophores incorporated into the same molecule exist in a variety of conformation/helicity combinations. The molecular structures are largely stabilized by local 1,3-CH/CO dipole–dipole interactions, while the crystal packing besides dispersive H...H interactions is mostly governed by multiple C—H...O(=C) and C—H...π interactions. The relatively small contribution of π...π interactions comes from a pairwise off-face stacking between naphthalimide rings or from pairwise carbonyl...π interactions. All these types of intermolecular interactions have been summarized quantitatively by means of a Hirshfeld surface analysis.
Dynamic proton disorder and the II–I structural phase transition in (NH4)3H(SO4)2
Authors: Sohn Yoo Jung , Loose Anja , Merz Michael , Sparta Karine , Klapper Helmut , Heger Gernot
Published: January 2009

X-ray powder diffraction, differential scanning calorimetry (DSC)/thermogravimetry (TG) and single-crystal neutron diffraction methods were used to investigate triammonium hydrogen disulfate (NH4)3H(SO4)2 (TAHS) in the temperature range between 293 and 493 K. The temperature-dependent X-ray powder diffraction measurements show a clear hysteresis of the I \leftrightarrow II phase transition of TAHS with transition temperatures of T
up = 412.9 (1) K on heating and of T
down = 402.6 (1) K on cooling. From the existence of hysteresis and from the jump-like changes of the lattice parameters, the I \leftrightarrow II phase transition of TAHS is considered to be first order. With DSC/TG measurements we confirmed that there is only one phase transition between 293 and 493 K. Through careful investigation on single crystals of TAHS using neutron diffraction, the correct space group (C2/c) of room-temperature TAHS-II phase was confirmed. Crystal structure analysis by single-crystal neutron diffraction showed a strongly elongated displacement ellipsoid of the proton which lies in the middle of the (SO4)H(SO4) dimer with \bar 1 local symmetry. The protons of the NH4 groups also show strongly enlarged anisotropic mean-square displacements. These findings are interpreted in terms of a characteristic proton disorder in the TAHS-II phase.
What limits fire? An examination of drivers of burnt area in Southern Africa
Authors: ARCHIBALD SALLY , ROY DAVID P. , Van WILGEN BRIAN W. , SCHOLES ROBERT J.
Published: January 2009

The factors controlling the extent of fire in Africa south of the equator were investigated using moderate resolution (500 m) satellite‐derived burned area maps and spatial data on the environmental factors thought to affect burnt area. A random forest regression tree procedure was used to determine the relative importance of each factor in explaining the burned area fraction and to address hypotheses concerned with human and climatic influences on the drivers of burnt area. The model explained 68% of the variance in burnt area. Tree cover, rainfall in the previous 2 years, and rainfall seasonality were the most important predictors. Human activities – represented by grazing, roads per unit area, population density, and cultivation fraction – were also shown to affect burnt area, but only in parts of the continent with specific climatic conditions, and often in ways counter to the prevailing wisdom that more human activity leads to more fire. The analysis found no indication that ignitions were limiting total burnt area on the continent, and most of the spatial variation was due to variation in fuel load and moisture. Split conditions from the regression tree identified (i) low rainfall regions, where fire is rare; (ii) regions where fire is under human control; and (iii) higher rainfall regions where burnt area is determined by rainfall seasonality. This study provides insights into the physical, climatic, and human drivers of fire and their relative importance across southern Africa, and represents the beginnings of a predictive framework for burnt area.
Environmental and economic factors determine the number of feral goats commercially harvested in Western Australia
Authors: Forsyth David M. , Parkes John P. , Woolnough Andrew P. , Pickles Greg , Collins Marnie , Gordon Ian
Published: January 2009

Many species of wildlife are harvested for sale but there are few time‐series analyses of the factors determining the number of animals harvested. Economic theory predicts that price paid per animal is likely to be an important determinant of the harvest, but prices paid for alternative activities could reduce the harvest, and environmental factors such as rainfall could either constrain or enhance the harvest.

About 1 million feral goats Capra hircus L. are commercially harvested annually in the semi‐arid rangelands of Australia, and there is much interest in how the harvest can be maximized so that the environmental impacts of the goats are minimized.

We developed 27 candidate models to explain monthly variation in the numbers of feral goats commercially harvested in Western Australia during July 1988 to June 2003. We fitted linear AR(1) models to the first 89 months of data and used Akaike's Information Criterion corrected for small sample size to identify the model(s) with substantial support. We then evaluated how much variation in the latter 88 months of the time series each model explained.

Almost 2·9 million feral goats were harvested in the study period. The two models with substantial support accounted for 70·5% and 70·6% of variation in the number of feral goats harvested during the first 89 months and 64·6% and 66·7% of variation in the subsequent 88 months. The models both included month of harvest and negative effects of rainfall in both the month of harvest and the previous month. One of the models also included a strong positive effect of the Australian Consumer Price Index‐adjusted average price paid per feral goat on the number of feral goats harvested, and this model had the most support when fitted to the entire time series.

 Synthesis and applications. This is the first study to demonstrate how both an environmental factor (rainfall) and an economic factor (average price paid per animal) can influence the size of a commercial wildlife harvest. Whilst managers can seldom modify environmental factors, our results suggest that the size of a wildlife harvest can be manipulated by altering the economics of the harvest.
Assuring the integrity of the family: being the father of a very low birth weight infant
Authors: Lee Tzu‐Ying , Lin Hung‐Ru , Huang Tsu‐Hsueh , Hsu Chyong‐Hsin , Bartlett Robin
Published: January 2009

Aim.  The purpose of this study was to explore the paternal role of fathers of very low birth weight infants during their first year of life.

Background.  Following birth, very low birth weight infants often require extended hospitalisation and long‐term care. The birth experience and the infant’s hospitalisation often overwhelm parents and may hinder the development of their parental roles. The father is known to be an important supporting figure for the mother, but most studies in Taiwan have focussed on mothers.

Design.  A qualitative design using a grounded theory approach was employed in this study.

Methods.  In‐depth interviews were conducted with a purposive sample of fathers during home visits.

Each father was interviewed twice at one to three months and seven to nine months after his very low birth weight infant’s discharge from the hospital. Data were analysed using constant comparison and repeated verification.

Results.  Twelve fathers were included in the study. During the first year of life of their very low birth weight infants, the fathers experienced ‘protecting the wife–baby dyad’, ‘concentrating on the child’s health and growth’, and ‘possessing a complete family’. Subcategories within each major category also emerged.

Conclusion.  In this study, Taiwanese fathers of very low birth weight infants learned different and broader dimensions of the paternal role and continually made adjustments to assure their family’s integrity.

Relevance to clinical practice.  These findings can help nurses understand paternal perceptions and behaviours related to having a very low birth weight infant and in turn help fathers adjust to their role.
The relationship between caregiver’s strain and social support among mothers with intellectually disabled children
Authors: Tsai Shu‐Mei , Wang Hsiu‐Hung
Published: January 2009

Aims and objectives. To explore caregiver’s strain, the relationship between social support and caregiver’s strain and the predictors of caregiver’s strain among mothers with school‐aged intellectually disabled children in Taiwan.

Background. Strain is a common condition among mothers who take care of intellectually disabled children; this correspondingly reduces their ability to care for children, thereby affecting the functioning of the entire family. Yet, there have been very few studies on caregivers of intellectually disabled children of school age.

Design. Cross‐section correlational design.

Methods. Data collection consisted of face‐to‐face interviews combined with a structured questionnaire. Instruments employed were the Caregiver Strain Index, Social Support Scale and three open‐ended questions. In total, 127 mothers completed the questionnaire.

Results. Results showed that mothers with intellectually disabled children had a rather high level of strain and received inadequate social support. Social support and strain had a significant and negative correlation. Stepwise regression analysis revealed that mothers’ health status, social support and amount of time spent as a caregiver, as well as the intellectually disabled children’s dependent degree of daily living activity, were major predictors of caregiver’s strain, which accounted for 38·4% of the total variance.

Conclusions. The results provide a guide for healthcare professionals in designing effective interventions and preventive care to reduce the level of strain in mothers with intellectually disabled children. This, in turn, could improve the quality of life of the mother and her family.

Relevance to clinical practice. In Taiwan, care of intellectually disabled children is primarily provided by family members. Therefore, we should emphasise family‐centred care to enable healthcare professionals to become more effective as case managers in local clinics, schools and communities.