bluuebunny/crossref_metadata_2025 huggingface dataset:
Basin‐scale fluid movement patterns revealed by veins: Wessex Basin, UK
Authors: Worden R. H. , Benshatwan M. S. , Potts G. J. , Elgarmadi S. M.
Published: April 2015

Calcite veins at outcrop in the Mesozoic, oil‐bearing Wessex Basin, UK, have been studied using field characterization, petrography, fluid inclusions and stable isotopes to help address the extent, timing and spatial and stratigraphic variability of basin‐scale fluid flow. The absence of quartz shows that veins formed at low temperature without an influence of hydrothermal fluids. Carbon isotopes suggest that the majority of vein calcite was derived locally from the host rock but up to one quarter of the carbon in the vein calcite came from CO2 from petroleum source rocks. Veins become progressively enriched in source‐rock‐derived CO2 from the outer margin towards the middle, indicating a growing influence of external CO2. The carbon isotope data suggest large‐scale migration of substantial amounts of CO2 around the whole basin. Fluid inclusion salinity data and interpreted water‐δ18O data show that meteoric water penetrated deep into the western part of the basin after interacting with halite‐rich evaporites in the Triassic section before entering fractured Lower and Middle Jurassic rocks. This large‐scale meteoric invasion of the basin probably happened during early Cenozoic uplift. A similar approach was used to reveal that, in the eastern part of the basin close to the area that underwent most uplift, uppermost Jurassic and Cretaceous rocks underwent vein formation in the presence of marine connate water suggesting a closed system. Stratigraphically underlying Upper Jurassic mudstone and Lower Cretaceous sandstone, in the most uplifted part of the basin, contain veins that resulted from intermediate behaviour with input from saline meteoric water and marine connate waters. Thus, while source‐rock‐derived CO2 seems to have permeated the entire section, water movement has been more restricted. Oil‐filled inclusions in vein calcite have been found within dominant E‐W trending normal faults, suggesting that these may have facilitated oil migration.
Hydrogeology of the Krafla geothermal system, northeast Iceland
Authors: Pope E. C. , Bird D. K. , Arnórsson S. , Giroud N.
Published: April 2015

The Krafla geothermal system is located in Iceland's northeastern neovolcanic zone, within the Krafla central volcanic complex. Geothermal fluids are superheated steam closest to the magma heat source, two‐phase at higher depths, and sub‐boiling at the shallowest depths. Hydrogen isotope ratios of geothermal fluids range from −87‰, equivalent to local meteoric water, to −94‰. These fluids are enriched in 18O relative to the global meteoric line by +0.5–3.2‰. Calculated vapor fractions of the fluids are 0.0–0.5 wt% (~0–16% by volume) in the northwestern portion of the geothermal system and increase towards the southeast, up to 5.4 wt% (~57% by volume). Hydrothermal epidote sampled from 900 to 2500 m depth has δD values from −127 to −108‰, and δ18O from −13.0 to −9.6‰. Fluids in equilibrium with epidote have isotope compositions similar to those calculated for the vapor phase of two‐phase aquifer fluids. We interpret the large range in δDEPIDOTE and δ18OEPIDOTE across the system and within individual wells (up to 7‰ and 3.3‰, respectively) to result from variable mixing of shallow sub‐boiling groundwater with condensates of vapor rising from a deeper two‐phase reservoir. The data suggest that meteoric waters derived from a single source in the northwest are separated into the shallow sub‐boiling reservoir, and deeper two‐phase reservoir. Interaction between these reservoirs occurs by channelized vertical flow of vapor along fractures, and input of magmatic volatiles further alters fluid chemistry in some wells. Isotopic compositions of hydrothermal epidote reflect local equilibrium with fluids formed by mixtures of shallow water, deep vapor condensates, and magmatic volatiles, whose ionic strength is subsequently derived from dissolution of basalt host rock. This study illustrates the benefits of combining phase segregation effects in two‐phase systems during analysis of wellhead fluid data with stable isotope values of hydrous alteration minerals when evaluating the complex hydrogeology of volcano‐hosted geothermal systems.
Frequency of androgenesis in Poa arachnifera × P. ligularis and P. poiformis hybridizations
Authors: Kindiger Bryan
Published: April 2015

The rapid generation of haploids in most species remains a relatively infrequent event, but is considered an important tool for the development of homozygous lines and an approach for cytoplasmic transfer across related species. Poa arachnifera ‘Texas bluegrass’ is known to occasionally produce androgenic haploid recoveries following hybridization with Poa secunda. However, little information regarding the frequency of such behavior following hybridization with other Poa species is available. This study was undertaken to determine the frequency of androgenic haploids following interspecific hybridization of P. arachnifera × Poa ligularis and P. arachnifera × Poa poiformis. The P. arachnifera × P. ligularis hybridizations exhibited a frequency of androgenic dihaploids (ADH) at 1.00%; where the P. arachnifera × P. poiformis hybridizations indicated a frequency of 0.69%. Results from this study suggest ADH generation is an infrequent but consistent behavior likely found in sexual P. arachnifera.
Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next‐generation sequencing
Authors: Appenzeller Silke , Gilissen Christian , Rijntjes Jos , Tops Bastiaan B J , Kastner‐van Raaij Annemiek , Hebeda Konnie M , Nissen Loes , Dutilh Bas E , van Krieken J Han J M , Groenen Patricia J T A
Published: April 2015

Aims

For patients who have multiple lymphomas with discordant pathology, it is relevant to determine whether there is one disseminated lymphoma or two unrelated lymphomas. Patients with disseminated, clonally related lymphomas are usually treated with the most powerful drugs available, while patients with unrelated (primary) lymphomas receive mainly standard first‐line therapies.

Methods and results

We used next‐generation sequencing on the Ion Torrent Personal Genome Machine to characterize the immunoglobulin heavy gene V–D–J rearrangements in two diagnostic tissue samples, including formalin‐fixed and paraffin‐embedded tissue, of two patients with iatrogenic immunodeficiency‐associated Epstein–Barr virus lymphoproliferative disorder, with ulcerative colitis as underlying disease. The immunoglobulin rearrangement sequences obtained by next‐generation sequencing revealed undoubtedly clonally related lesions in two tissue biopsies that were taken over time in the first patient, which is concordant with disseminated lymphoma. The other patient showed two clonally unrelated lesions, which is incompatible with clonal dissemination. This information was not inferred from evaluation of the heavy and light chain rearrangements by fragment analysis, which is currently the gold standard.

Conclusion

Our study demonstrates the diagnostic application of next‐generation sequencing of immunoglobulin rearrangement assessment in pathology for clinical decision‐making in patients with several simultaneous or subsequent lymphoproliferations.
TIM‐1 rs41297579 G>A (−1454) and TIM‐4 rs7700944 gene polymorphisms as possible risk factor for rheumatoid arthritis: relation to activity and severity
Authors: Mosaad Y. M. , El‐bassiony S. R. , El‐Ghaweet A. E. , Elhindawy M. M. , EL‐Deek B. S. , Sultan W. A.
Published: April 2015

This study was aimed to evaluate the impact of both TIM‐1 rs41297579 G>A (−1454) and TIM‐4 rs7700944 polymorphisms on susceptibility to rheumatoid arthritis (RA) in a cohort of Egyptian population and to evaluate for the first time their relation to activity, severity, disease‐related disability and erosion. TIM‐1 rs41297579 G>A (−1454) and TIM‐4 rs7700944 gene polymorphisms were typed by RFLP for 128 patients with RA and 125 healthy controls. The A allele, A‐containing genotypes (GA and AA) of the TIM‐4 and GA haplotype were present with significant higher frequency in patients with RA than healthy controls (Pc < 0.001). These findings suggest that the A allele, A‐containing genotypes (GA and AA) and GA haplotype may be a susceptibility risk factor for RA [OR = 5.83 (3.6–9.4), OR = 9.41 (5.0–17.6) and OR = 4.21 (1.07–19.2), respectively]. No associations were found between TIM genotypes and disease activity, severity or presence of erosion. However, the RA patients with GA genotype of TIM‐4 have higher grade of rheumatoid factor (RF) positivity (P = 0.018), and have worse disease‐related disability (P = 0.007) and worse pain (0.025). TIM‐4 rs7700944 and not TIM‐1 rs41297579 G>A (−1454) is associated with RA in the present cohort of Egyptian and may be a risk factor for development of RA in Egyptian. Both SNPs have no effect on disease activity, severity or erosion. However, TIM‐4 GA genotype is associated with higher grade of RF positivity and worse disease‐related disability and pain.
Far‐Red‐Emitting BiOCl:Eu3+ Phosphor with Excellent Broadband NUV‐Excitation for White‐Light‐Emitting Diodes
Authors: Li Yongjin , Zhao Zongyan , Song Zhiguo , Wan Ronghua , Qiu Jianbei , Yang Zhengwen , Yin Zhaoyi , Liu Xuee , Liu Qun , Zhou Yuting
Published: April 2015

Rare‐earth ion‐doped semiconducting phosphor has attracted extensive attention due to the ability to achieve efficient luminescence through the host sensitization. Here, we present a new type red‐emitting Eu3+ ‐doped BiOCl phosphors possessing a broad excitation band in the near‐ultraviolet (NUV) region. Experimental measurements and theoretical calculations confirm that Eu3+ ion dopants result in forming impurity energy level near valence band, and the excellent broadband NUV‐exciting ability of Eu3+ ion is due to the electronic transitions of BiOCl band gap. Moreover, the highest emission intensity of the phosphors is from the 5D0 → 7F4 transition of Eu3+ around 699 nm (far‐red) through whether host excitation or direct Eu3+ ions excitation, which lie in the particular structure of BiOCl crystals. Our results indicate that the Eu3+ ‐doped BiOCl crystals show great potential as red phosphors for white‐light‐emitting diodes.
Do Sovereign Re‐Ratings Destabilize Equity Markets during Financial Crises? New Evidence from Higher Return Moments
Authors: Brooks Robert , Faff Robert , Treepongkaruna Sirimon , Wu Eliza
Published: April 2015

This study investigates the effects of S&P's sovereign re‐ratings on the higher moments of equity market returns over recent financial crises. Using a set of intraday stock market index prices and sovereign credit ratings for a sample of 36 countries that experienced sovereign rating changes over the period from 1996 to 2013, we find that the higher moments of stock market returns are significantly more responsive to sovereign re‐ratings during financial crises, but the effects on stock markets are not the same across different financial crises. The effects during crises are, however, magnified for large downgrades and those that are associated with a loss of investment grade status. We find that there are asymmetric effects during financial crises in that downgrades are consistently more significant than upgrades in increasing realized volatility and realized kurtosis. Both upgrades and downgrades affect realized skewness in times of crises in the expected direction.
MicroRNA‐181c targets Bcl‐2 and regulates mitochondrial morphology in myocardial cells
Authors: Wang Hongjiang , Li Jing , Chi Hongjie , Zhang Fan , Zhu Xiaoming , Cai Jun , Yang Xinchun
Published: April 2015

Apoptosis is an important mechanism for the development of heart failure. Mitochondria are central to the execution of apoptosis in the intrinsic pathway. The main regulator of mitochondrial pathway of apoptosis is Bcl‐2 family which includes pro‐ and anti‐apoptotic proteins. MicroRNAs are small noncoding RNA molecules that regulate gene expression by inhibiting mRNA translation and/or inducing mRNA degradation. It has been proposed that microRNAs play critical roles in the cardiovascular physiology and pathogenesis of cardiovascular diseases. Our previous study has found that microRNA‐181c, a miRNA expressed in the myocardial cells, plays an important role in the development of heart failure. With bioinformatics analysis, we predicted that miR‐181c could target the 3′ untranslated region of Bcl‐2, one of the anti‐apoptotic members of the Bcl‐2 family. Thus, we have suggested that miR‐181c was involved in regulation of Bcl‐2. In this study, we investigated this hypothesis using the Dual‐Luciferase Reporter Assay System. Cultured myocardial cells were transfected with the mimic or inhibitor of miR‐181c. We found that the level of miR‐181c was inversely correlated with the Bcl‐2 protein level and that transfection of myocardial cells with the mimic or inhibitor of miR‐181c resulted in significant changes in the levels of caspases, Bcl‐2 and cytochrome C in these cells. The increased level of Bcl‐2 caused by the decrease in miR‐181c protected mitochondrial morphology from the tumour necrosis factor alpha‐induced apoptosis.
Numerical Modeling of Heat and Mass Transfer during Contact Baking of Flat Bread
Authors: Sadeghi Farzad , Hamdami Nasser , Shahedi Mohammad , Rafe Ali
Published: April 2015

A multiphase model was developed to simulate heat and mass transfer during the baking process of flat bread (Sangak bread) by considering volume changes. In the proposed model, the equations of heat and mass transfer for liquid (water) and gas (vapor andCO2) phases were developed based onFourier's,Fick's andDarcy's laws, respectively. In addition, the effect of evaporation–condensation phenomenon was considered using the nonequilibrium relation of evaporation rate in the mass and heat transfer equations. The quantity of specific heat and density of each mesh was predicted using series and parallel models, and values of unknown parameters were estimated using the standard least square method. The nonlinear partial differential equations of the model were solved by using the finite element method byCOMSOLMultiphysics software. The changes in bread thickness were determined by ImageJsoftware. The model validation was also accomplished by comparing the predicted temperature and moisture content with the experimental results. The highR2and the low root mean squared error between experimental and predicted data confirmed the validity of the developed mathematical model.

Practical Applications

The uniformity of the product quality and the energy loss during the baking process has always been considered as a great challenge in the baking industry. In recent years, there has been increasing demand for minimally processed and near‐fresh quality products. To produce the part‐baked Sangak bread, the dough fully processes and baking occurs to at level in which, the texture properly forms and low color changes occur. Nowadays, it is essential to find methods based on equations, mathematical modeling and engineering principles to improve process control. In order to develop these models, the profound understanding of the procedures during the baking, particularly, mass and energy transfer are essential. Since, there are few researches on evaporation‐condensation and volume change in contact baking; it is important to understand its mechanism for exploiting this phenomenon in the food industries.
Microbiological and Physicochemical Quality Changes in Frankfurters Made from Jumbo Squid (Dosidicus gigas) Mantle Muscle in the Presence and Absence of a Natural Antimicrobial Agent
Authors: Ramírez‐Suárez Juan Carlos , Pacheco‐Aguilar Ramón , Scheuren‐Acevedo Susana María , García‐Sánchez Guillermina , Carvallo‐Ruiz Gisela , Lugo‐Sánchez María Elena , Cumplido‐Barbeitia German , Jiménez‐Ruiz Edgar Iván
Published: April 2015

This study aimed to evaluate the effect of a natural antimicrobial agent (Pronat) on selected quality indicators during the shelf life of vacuum‐packed frankfurters made from jumbo squid (Dosidicus gigas) muscle. Frankfurters with and without Pronat (0.1%) were vacuum‐packed and stored at 2–4C for up to 28 days. The physicochemical parameters (water loss, pH, thiobarbituric acid value, peroxide value, moisture, texture [texture profile analysis and sharing force], folding test performance, water‐holding capacity [WHC], drip loss and color) as well as the microbial counts (total aerobic and anaerobic count, total and fecal coliform) of the samples were assessed. The samples with Pronat were physicochemically stable and in good microbiological condition up to 21 days compared with the control. The main changes were attributed to color, WHC and drip loss. The Pronat concentration used in squid frankfurters greatly improved their microbiological shelf life but did not considerably improve the physicochemical quality indicators assessed in the present study.

Practical Applications

At the present time and in response to a market niche, natural and healthier foods are sought. Therefore, natural antimicrobial agent is an alternative to be used in the production of jumbo squid frankfurters, generating a healthy product with an extended shelf life.
A Luting Technique for Passive Fit of Implant‐Supported Fixed Dentures
Authors: Menini Maria , Dellepiane Elena , Pera Paolo , Bevilacqua Marco , Pesce Paolo , Pera Francesco , Tealdo Tiziano
Published: April 2015

Several factors contribute to distortion of implant prostheses during fabrication and could prevent passive, accurate adaptation between implants and implant frameworks. The misfit between implants and restorative components may be significant and possibly lead to biologic or mechanical complications. The aim of this article is to describe a laboratory luting technique used to lute implant cylinders to metal frameworks in implant prostheses. This technique provides accurate, passive fits. According to this technique, titanium implant cylinders provided with corresponding external castable cylinders are used. Implant cylinders are screwed into the analogs in the master cast while the castable cylinders on top are splinted together using castable resin to realize a castable resin pattern. After casting, the framework is adjusted and cemented to the titanium cylinders on the master cast. Due to its ease and quickness of use and clinical efficiencies, this technique is deemed particularly useful in immediate loading rehabilitations.
Saponins from P
anax japonicus attenuate D-galactose-induced cognitive impairment through its anti-oxidative and anti-apoptotic effects in rats
Authors: Wang Ting , Di Guojie , Yang Li , Dun Yaoyan , Sun Zhiwei , Wan Jingzhi , Peng Ben , Liu Chaoqi , Xiong Guangrun , Zhang Changcheng , Yuan Ding
Published: April 2015

Objective

To investigate the neuroprotective effects of saponins from Panax japonicus (SPJ) on D-galactose (D-gal)-induced brain ageing, and further explore the underlying mechanisms.

Methods

SPJ were analysed using high-pressure liquid chromatography. Male Wistar rats weighing 200 ± 20 g were randomly divided into four groups: control group (saline), D-gal-treated group (400 mg/kg, subcutaneously), D-gal + SPJ groups (50, 100 and 200 mg/kg, orally) and vitamin E group (100 mg/kg). Rats were injected corresponding drugs once daily for 8 weeks. Neuroprotective effects of SPJ were evaluated by Morris water maze, histopathological observations, biochemical assays, western blot analysis and quantitative real-time polymerase chain reaction (PCR) analysis in vivo as well as reactive oxygen species (ROS) measurement and apoptosis assay in vitro.

Key findings

Our present study showed that D-gal had a neurotoxic effect in rats and in SH-SY5Y cells due to oxidative stress induction, including decreased total anti-oxidant capacity, superoxide dismutase (SOD) and glutathione peroxidase activity, ultimately leading to spatial learning and memory impairment in rats and ROS accumulation in SH-SY5Y cells. SPJ improved spatial learning and memory deficits, attenuated hippocampus histopathological injury and restored impaired anti-oxidative as well as anti-apoptotic capacities in D-gal-induced ageing rats. In addition, SPJ remarkably decreased lipofuscin levels, increased hippocampus nuclear factor erythroid 2-related factor 2 (Nrf2) and silent mating type information regulation 2 homologue (SIRT1) protein levels and anti-oxidant genes expression such as manganese superoxide dismutase (Mn-SOD), heme oxygenase (HO-1), NAD(P)H quinone oxidoreductase 1 (NQO1) and cysteine ligase catalytic (GCLC) in D-gal-induced brain ageing.

Conclusions

Our data suggested that D-gal induced multiple molecular and functional changes in brain similar to natural ageing process. SPJ protected brain from D-gal-induced neuronal injury through decreasing oxidative stress and apoptosis, and ultimately improving cognitive performance in D-gal-induced brain ageing. It is possibly related to Nrf2 and SIRT1-mediated anti-oxidant signalling pathways.
Effects of dietary supplementation of selenium‐enriched probiotics on production performance and intestinal microbiota of weanling piglets raised under high ambient temperature
Authors: Lv C. H. , Wang T. , Regmi N. , Chen X. , Huang K. , Liao S. F.
Published: April 2015

This study was designed to evaluate the efficacy of selenium‐enriched probiotics (SeP) on production performance and intestinal microbiota of piglets raised under high ambient temperature. Forty‐eight cross‐bred weanling piglets (28 days old), randomly allotted into 12 pens (four piglets/pen) and four dietary treatments (three pens/treatment group), were fed ad libitum for 42 days a basal diet (Con) or the basal diet supplemented with probiotics (Pro), sodium selenite (ISe) or a SeP preparation. Blood and faecal samples were collected on days 0, 14, 28 and 42 post‐treatment. The SeP group had higher final BW (p < 0.05), greater ADG (p < 0.05) and lower FCR (p < 0.01) than the Pro, ISe or Con group. The diarrhoea incidence rate of either SeP or Pro group was lower (p < 0.01) than the ISe or Con group. Blood Se concentration and GSH‐Px activity were both higher (p < 0.01) in the SeP than in the Pro, ISe or Con group. On days 28 and 42, the serum concentrations of T3 were higher (p < 0.01) and T4 lower (p < 0.01) in the SeP than in the ISe group, and the T3 and T4 concentrations in the ISe group, in turn, were higher (p < 0.05) and lower (p < 0.01), respectively, than in the Pro or Con group. Also on days 28 and 42, the faecal counts of lactobacillus bacteria were higher (p < 0.01) while Escherichia coli lower (p < 0.01) in the SeP or Pro group as compared to the ISe or Con group. The results of RFLP showed that the faecal microbial flora in the SeP group changed the most (numerically) as compared to the Pro or ISe group. These results suggest that the SeP product may serve as a better alternative to antibiotics than the solo probiotics for using as a growth promoter for weanling piglets.
Remoteness, race and social disadvantage: disparities in hepatocellular carcinoma incidence and survival in Queensland, Australia
Authors: Clark Paul J. , Stuart Katherine A. , Leggett Barbara A. , Crawford Darrell H. , Boyd Peter , Fawcett Jonathan , Whiteman David C. , Baade Peter D.
Published: April 2015

Background & Aims

Incidence and mortality of hepatocellular carcinoma (HCC) is increasing globally, but varies between countries and regions. To target scarce resources to most need, clinical services must be informed by regional epidemiology. Using population‐based data, we sought to document the incidence and mortality of HCC in Queensland, Australia, a state occupying a vast land area with diverse at‐risk subpopulations.

Methods

Using population‐based data from 1996 to 2011, the age‐standardised incidence rate (ASR), annual percentage change (APC) and survival of HCC in Queensland were assessed with negative binomial regression, Kaplan–Meier and Cox survival analysis. Spatial patterns of HCC incidence and survival and relevant predictors were mapped.

Results

Thousand six hundred and twenty HCCs were diagnosed during this study period, with an overall ASR of 2.00‐cases/1000 population. ASR increased by 3.5% per year, (95% CI: 2.1 to 5.0), P < 0.001) among males to 5.6/100,000 in 2011 and a non‐significant increase of 2.6% per year, (95% CI = −0.7 to 6.0), P = 0.111) among females to 1.6/100,000 in 2011. Higher incidence was associated with male gender, older age, major city residence and proportionally higher area Indigenous population. Thousand and two hundred and eighty‐seven patients died. Median survival was approximately 10 months. Five‐year survival improved from 18% in 1996–2000 to 24% in 2006–2011 (P < 0.001). Poorer survival was associated with older age, less recent period of diagnosis, lower hepatitis B prevalence in country of origin and greater area‐level social disadvantage.

Conclusions

Over this study period, HCC incidence increased significantly. HCC survival improved but remains poor. Social determinants are critical to HCC epidemiology.
Does the Excess Entry Theorem Hold in a Differentiated Oligopoly?
Authors: Kagitani Koichi , Ohkawa Takao , Okamura Makoto
Published: April 2015

Though it is generally believed that increasing competition improves social welfare, we are able to show with a Shubik–Levitan demand function for differentiated goods that this is not always the case. Under Cournot and Bertrand competition, market entry increases the equilibrium total output and lowers the equilibrium price in the case of substitutes, but it reduces the total output and raises the price in the case of complements. In the long run, the equilibrium number of firms is excessive and the equilibrium cannot achieve even the second‐best social welfare under either type of competition, regardless of product substitutability or complementarity.
Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes
Authors: Fung Herman K. H. , Gadd Morgan S. , Drury Thomas A. , Cheung Samantha , Guss J. Mitchell , Coleman Nicholas V. , Matthews Jacqueline M.
Published: April 2015

Haloalkane dehalogenases (HLDs) catalyse the hydrolysis of haloalkanes to alcohols, offering a biological solution for toxic haloalkane industrial wastes. Hundreds of putative HLD genes have been identified in bacterial genomes, but relatively few enzymes have been characterised. We identified two novel HLDs in the genome of Mycobacterium rhodesiae strain JS60, an isolate from an organochlorine‐contaminated site: DmrA and DmrB. Both recombinant enzymes were active against C2–C6 haloalkanes, with a preference for brominated linear substrates. However, DmrA had higher activity against a wider range of substrates. The kinetic parameters of DmrA with 4‐bromobutyronitrile as a substrate were Km = 1.9 ± 0.2 mM, kcat = 3.1 ± 0.2 s−1. DmrB showed the highest activity against 1‐bromohexane. DmrA is monomeric, whereas DmrB is tetrameric. We determined the crystal structure of selenomethionyl DmrA to 1.7 Å resolution. A spacious active site and alternate conformations of a methionine side‐chain in the slot access tunnel may contribute to the broad substrate activity of DmrA. We show that M. rhodesiae JS60 can utilise 1‐iodopropane, 1‐iodobutane and 1‐bromobutane as sole carbon and energy sources. This ability appears to be conferred predominantly through DmrA, which shows significantly higher levels of upregulation in response to haloalkanes than DmrB.
No‐sedation during mechanical ventilation: impact on patient's consciousness, nursing workload and costs
Authors: Laerkner Eva , Stroem Thomas , Toft Palle
Published: April 2015

Background

Evidence is growing that less or no‐sedation is possible and beneficial for patients during mechanical ventilation.

Aim

To investigate if there was a difference in patient consciousness and nursing workload comparing a group of patients receiving no‐sedation with a group of sedated patients with daily wake up, and also to estimate economic consequences of a no‐sedation strategy.

Design and methods

Data were collected during a prospective trial of 140 mechanically ventilated patients randomized to either no‐sedation or to sedation with daily wake up. From day 1 to 7 in the intensive care unit (ICU), patients were Richmond Agitation and Sedation Scale (RASS) scored, nursing workload was measured with the Nursing Care Recording System (NCR11) and nurse's self‐assessment of workload was reported on a Numeric Rating Scale from 1 (low) to 10 (high).

Results

Patients from the no‐sedation group had a median RASS score of −0·029 compared with −2 in the sedated group (P < 0·00001). The NCR11 scores were higher in the sedated group compared with the no‐sedation group: 19·054 versus 17·05 (P = 0·00001). The nurses self‐reported workload was the same in both groups (P = 0·085). Because of a shorter ICU stay and shorter hospital length of stay in the no‐sedation group, we estimated that there will be no cost benefit with the use of sedation and a higher patient to nurse ratio.

Conclusion

Patients receiving no‐sedation were more awake with a RASS score close to zero, compared with patients receiving sedation and daily wake up. Nurses reported no difference in self‐assessed workload between the no‐sedation and sedated group of patients.

Relevance to clinical practice

Patients receiving no‐sedation are more awake during their stay in ICU. There might be a potential economical saving with the use of a 1:1 nurse‐patient ratio and no‐sedation compared with sedation and a 1:2 nurse‐patient ratio.
Dissecting the molecular signatures of apical cell‐type shoot meristems from two ancient land plant lineages
Authors: Frank Margaret H. , Edwards Molly B. , Schultz Eric R. , McKain Michael R. , Fei Zhangjun , Sørensen Iben , Rose Jocelyn K. C. , Scanlon Michael J.
Published: April 2015

Shoot apical meristem (SAM) structure varies markedly within the land plants. The SAMs of many seedless vascular plants contain a conspicuous inverted, pyramidal cell called the apical cell (AC), which is unidentified in angiosperms.

In this study, we use transcriptomic sequencing with precise laser microdissections of meristem subdomains to define the molecular signatures of anatomically distinct zones from the AC‐type SAMs of a lycophyte (Selaginella moellendorffii) and a monilophyte (Equisetum arvense). The two model species for this study represent vascular plant lineages that diverged > 400 million yr ago.

Our data comprise comprehensive molecular signatures for the distinct subdomains within AC‐type SAMs, an anatomical anomaly whose functional significance has been debated in the botanical literature for over two centuries.

Moreover, our data provide molecular support for distinct gene expression programs between the AC‐type SAMs of Selaginella and Equisetum, as compared with the SAM transcriptome of the angiosperm maize. The results are discussed in light of the functional significance and evolutionary success of the AC‐type SAM within the embryophytes.
The contribution of phenotypic plasticity to complementary light capture in plant mixtures
Authors: Zhu Junqi , van der Werf Wopke , Anten Niels P. R. , Vos Jan , Evers Jochem B.
Published: April 2015

Interspecific differences in functional traits are a key factor for explaining the positive diversity–productivity relationship in plant communities. However, the role of intraspecific variation attributable to phenotypic plasticity in diversity–productivity relationships has largely been overlooked. By taking a wheat (Triticum aestivum)–maize (Zea mays) intercrop as an elementary example of mixed vegetation, we show that plasticity in plant traits is an important factor contributing to complementary light capture in species mixtures.

We conceptually separated net biodiversity effect into the effect attributable to interspecific trait differences and species distribution (community structure effect), and the effect attributable to phenotypic plasticity. Using a novel plant architectural modelling approach, whole‐vegetation light capture was simulated for scenarios with and without plasticity based on empirical plant trait data.

Light capture was 23% higher in the intercrop with plasticity than the expected value from monocultures, of which 36% was attributable to community structure and 64% was attributable to plasticity. For wheat, plasticity in tillering was the main reason for increased light capture, whereas for intercropped maize, plasticity induced a major reduction in light capture.

The results illustrate the potential of plasticity for enhancing resource acquisition in mixed stands, and indicate the importance of plasticity in the performance of species‐diverse plant communities.
Global convergence in leaf respiration from estimates of thermal acclimation across time and space
Authors: Vanderwel Mark C. , Slot Martijn , Lichstein Jeremy W. , Reich Peter B. , Kattge Jens , Atkin Owen K. , Bloomfield Keith J. , Tjoelker Mark G. , Kitajima Kaoru
Published: April 2015

Recent compilations of experimental and observational data have documented global temperature‐dependent patterns of variation in leaf dark respiration (R), but it remains unclear whether local adjustments in respiration over time (through thermal acclimation) are consistent with the patterns in R found across geographical temperature gradients.

We integrated results from two global empirical syntheses into a simple temperature‐dependent respiration framework to compare the measured effects of respiration acclimation‐over‐time and variation‐across‐space to one another, and to a null model in which acclimation is ignored. Using these models, we projected the influence of thermal acclimation on: seasonal variation in R; spatial variation in mean annual R across a global temperature gradient; and future increases in R under climate change.

The measured strength of acclimation‐over‐time produces differences in annual R across spatial temperature gradients that agree well with global variation‐across‐space. Our models further project that acclimation effects could potentially halve increases in R (compared with the null model) as the climate warms over the 21st Century.

Convergence in global temperature‐dependent patterns of R indicates that physiological adjustments arising from thermal acclimation are capable of explaining observed variation in leaf respiration at ambient growth temperatures across the globe.
Host genotype is an important determinant of the cereal phyllosphere mycobiome
Authors: Sapkota Rumakanta , Knorr Kamilla , Jørgensen Lise Nistrup , O'Hanlon Karen A. , Nicolaisen Mogens
Published: April 2015

The phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking.

Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum × Secale) was studied using next‐generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored.

In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo‐cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified.

Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host‐specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host‐specific pathogens live in a ‘sea’ of nonspecific fungi.
Integrating movement in academic classrooms: understanding, applying and advancing the knowledge base
Authors: Webster C. A. , Russ L. , Vazou S. , Goh T. L. , Erwin H.
Published: April 2015

In the context of comprehensive and coordinated approaches to school health, academic classrooms have gained attention as a promising setting for increasing physical activity and reducing sedentary time among children. The aims of this paper are to review the rationale and knowledge base related to movement integration in academic classrooms, consider the practical applications of current knowledge to interventions and teacher education, and suggest directions for future research. Specifically, this paper (i) situates movement integration amid policy and research related to children's health and the school as a health‐promoting environment; (ii) highlights the benefits of movement integration; (iii) summarizes movement integration programs and interventions; (iv) examines factors associated with classroom teachers’ movement integration; (v) offers strategies for translating research to practice and (vi) forwards recommendations for future inquiry related to the effectiveness and sustainability of efforts to integrate movement into classroom routines. This paper provides a comprehensive resource for developing state‐of‐the‐art initiatives to maximize children's movement in academic classrooms as a key strategy for important goals in both education and public health.
Soybean seeds overexpressing asparaginase exhibit reduced nitrogen concentration
Authors: Pandurangan Sudhakar , Pajak Agnieszka , Rintoul Tara , Beyaert Ronald , Hernández‐Sebastià Cinta , Brown Daniel C. W. , Marsolais Frédéric
Published: April 2015

In soybean seed, a correlation has been observed between the concentration of free asparagine at mid‐maturation and protein concentration at maturity. In this study, a Phaseolus vulgaris K+‐dependent asparaginase cDNA, PvAspG2, was expressed in transgenic soybean under the control of the embryo specific promoter of the β‐subunit of β‐conglycinin. Three lines were isolated having high expression of the transgene at the transcript, protein and enzyme activity levels at mid‐maturation, with a 20‐ to 40‐fold higher asparaginase activity in embryo than a control line expressing β‐glucuronidase. Increased asparaginase activity was associated with a reduction in free asparagine levels as a percentage of total free amino acids, by 11–18%, and an increase in free aspartic acid levels, by 25–60%. Two of the lines had reduced nitrogen concentration in mature seed as determined by nitrogen analysis, by 9–13%. Their levels of extractible globulins were reduced by 11–30%. This was accompanied by an increase in oil concentration, by 5–8%. The lack of change in nitrogen concentration in the third transgenic line was correlated with an increase in free glutamic acid levels by approximately 40% at mid‐maturation.
Citizen Participation in Budgeting: A Trade‐Off between Knowledge and Inclusiveness?
Authors: Hong Sounman
Published: April 2015

Research on citizen participation has noted a tension between fostering an inclusive policy‐making process and simultaneously maintaining a competent pool of participating citizens. This article investigates the implications of this trade‐off by testing the impact of measured levels of inclusiveness and participating citizens’ knowledgeability on two performance metrics: citizen engagement and process efficiency. Results indicate that although inclusiveness may be negatively associated with the level of engagement, both knowledgeability and inclusiveness are positively associated with process efficiency. Overall, the findings suggest that policy makers can pursue the democratic ideal of opening policy making to the citizenry while still maintaining an efficient process.
Empowering Local Action through Neo‐Endogenous Development; The Case of LEADER in England
Authors: Bosworth Gary , Annibal Ivan , Carroll Terry , Price Liz , Sellick Jessica , Shepherd John
Published: April 2015

Neo‐endogenous rural development depends on ‘bottom‐up’ activities that integrate external influences to increase local potential. This local focus calls for local knowledge, local resources and the engagement of local people to be central to development processes. Based on data from an evaluation of LEADER in England, we explore the scope for local control and the effective means of creating local empowerment within the neo‐endogenous model. Interviews were held with policy actors and beneficiaries of funding across 20 of the 64 Local Action Groups in England. These highlighted a great diversity of projects generating an equally diverse range of outcomes. However, capturing their full value was problematic, suggesting that new approaches to evaluation should be explored to increase local control of the development process. Findings also indicate that the negotiation between top‐down and bottom‐up, and local and external influences is an ongoing process. Through this process, local learning has empowered local actors to develop flexible approaches tailored to their localities, but local empowerment is more effective when top‐down parameters are clearly established.
Estimating Slavery Reparations: Present Value Comparisons of Historical Multigenerational Reparations Policies
Authors: Craemer Thomas
Published: April 2015

Objective

I investigate two problems regarding multigenerational reparations: legal obstacles caused by the passage of time and economic difficulties in obtaining realistic present value estimates.

Methods

To investigate legal precedents, I trace the French spoliation claims, which were paid over a period of 123 years, and Haiti's independence debt, which was paid over 156 years. To investigate present value estimation, I compare existing slavery reparations estimates based on slave prices as expected future income to alternative estimates based on the number of unremunerated work hours multiplied with historical free labor market wages.

Results

I estimate the present value of U.S. slave labor in 2009 dollars to range from $5.9 to $14.2 trillion. Historical precedents suggest that political rather than narrowly legal processes will determine any ultimate claims.

Conclusions

Neither problems nor solutions associated with multigenerational reparations are new. New is the estimation method and the resulting upward correction of reparations estimates.
Rational Use of Cognitive Resources: Levels of Analysis Between the Computational and the Algorithmic
Authors: Griffiths Thomas L. , Lieder Falk , Goodman Noah D.
Published: April 2015

Marr's levels of analysis—computational, algorithmic, and implementation—have served cognitive science well over the last 30 years. But the recent increase in the popularity of the computational level raises a new challenge: How do we begin to relate models at different levels of analysis? We propose that it is possible to define levels of analysis that lie between the computational and the algorithmic, providing a way to build a bridge between computational‐ and algorithmic‐level models. The key idea is to push the notion of rationality, often used in defining computational‐level models, deeper toward the algorithmic level. We offer a simple recipe for reverse‐engineering the mind's cognitive strategies by deriving optimal algorithms for a series of increasingly more realistic abstract computational architectures, which we call “resource‐rational analysis.”
Identification by real‐timePCRwithSYBRGreen ofLeishmaniaspp. andSerratia marcescensin canine ‘sterile’ cutaneous nodular lesions
Authors: Cornegliani Luisa , Corona Antonio , Vercelli Antonella , Roccabianca Paola
Published: April 2015

Background

Noninfectious, non‐neoplastic, nodular to diffuse, so‐called ‘sterile’ granulomatous/pyogranulomatous skin lesions (SGPSLs) are infrequently identified in dogs and may represent a diagnostic challenge. Their correct identification is based on history, histopathology and absence of intralesional foreign bodies and micro‐organisms.

Hypothesis/Objectives

The aim of this study was to investigate the presence ofLeishmaniaspp.,Mycobacteriumspp.,Serratia marcescensandNocardiaspp. by real‐timePCRin canine nodular skin lesions histologically diagnosed as putatively sterile.

Methods

Formalin‐fixed skin biopsies were collected from 40 dogs. All samples were associated with anSGPSLdiagnosis characterized by multifocal, nodular to diffuse, periadnexal and perifollicular pyogranulomas/granulomas. Neither micro‐organisms nor foreign bodies were detected with haematoxylin and eosin staining, under polarized light. Further analyses included periodic acidSchiff,Ziehl–Neelsen,FiteFaraco,Giemsa andGram histochemical stains; anti‐BacillusCalmette–Guérin (BCG) andLeishmaniaspp. immunohistochemistry; and real‐timePCRanalysis forLeishmaniaspp.,Mycobacteriumspp.,S. marcescensandNocardiaspp.

Results

Special stains andBCG/immunohistochemistry were negative in all samples. Real‐timePCRwas positive forLeishmaniaspp. in four of 40 biopsies and forS. marcescensin two of 40 samples. Real‐timePCRforMycobacteriumspp. andNocardiaspp. was negative. No correlation between real‐timePCRpositivity and a specific histological pattern was identified.

Conclusions and clinical importance

Leishmaniaspp. have been previously identified as possible agents of certainSGPSLs, while the involvement ofS. marcescenshas not been investigated previously. According to our findings,Serratiaspp. should be included in the list of agents possibly associated with a subgroup of granulomatous/pyogranulomatous skin lesions in dogs.
Retrospective evaluation of ProcalAmine administration in a population of hospitalized ICU dogs: 36 cases (2010–2013)
Authors: Olan Natasha V. , Prittie Jennifer
Published: April 2015

Objective

To describe the use of ProcalAmine as a source of parenteral nutrition in hospitalized dogs and to report complications possibly referable to its use.

Design

Retrospective study.

Settings

Private veterinary teaching hospital.

Animals

Thirty‐six dogs hospitalized in ICU receiving ProcalAmine between October 2010 and March 2013.

Interventions

None.

Measurements and Main Results

The most common underlying disease process in this population of dogs was trauma (n = 8). Median duration of administration was 4 days and median resting energy requirement provided via ProcalAmine was 33%. ProcalAmine was administered via central catheters in 86% of cases and via peripheral catheters in 14% of cases. The overall mechanical complication rate was 19%. Metabolic complications possibly associated with ProcalAmine administration were documented in 12/36 dogs. Hyponatremia was most commonly identified (n = 6) followed by hyperglycemia (n = 4), hypochloremia (n = 2), azotemia (n = 2), metabolic alkalosis (n = 2), hyperchloremia (n = 1), and metabolic acidosis (n = 1).

Conclusion

ProcalAmine appears to be relatively safe and a viable option for parenteral nutrition in ill and injured dogs. Due to the potential for electrolyte derangements and other metabolic complications, daily monitoring of these parameters is advisable.