bluuebunny/crossref_metadata_2025 huggingface dataset:
The Relative Efficiency of Hired and Family Labour in Bangladesh Agriculture
Authors: Chowdhury Nasima Tanveer
Published: May 2013

In Bangladesh, labour supply is abundant, but land for cultivation is shrinking mainly because of growing human settlement and urbanisation with a very high population density. This study examines whether labour use is efficient in Bangladesh agriculture and analyses the relative efficiency of hired and family labour for three crop seasons. Production functions are estimated using data collected by International Rice Research Institute on expenditures of agricultural inputs and returns on investment from a nationally representative sample of 1928 farm households from all 64 districts of Bangladesh. Results show that family labour is more productive than hired labour in Bangladesh agriculture, which has important policy implications for the rural labour market. Copyright © 2013 John Wiley & Sons, Ltd.
Investigation of the methanogen‐related archaeal population structure in shallow sediments of the Pearl River Estuary, Southern China
Authors: Chen Jinquan , Wang Fengping , Zheng Yanping , Jiang Lijing , Xiao Xiang
Published: May 2013

Few studies have specifically dealt so far with methanogen‐related archaea in estuarine sediments. In this study, methanogen‐related archaeal populations were investigated by 16S rRNA gene clone library, T‐RFLP analysis, and methanogen enrichment in Pearl River estuarine sediments. The majority of obtained sequences in clone libraries and T‐RF peaks from T‐RFLP analysis were assigned mainly to Methanosaeta, Methanomicrobiales, and Methanosarcinales/ANME. The fragments of Methanosarcinales/ANME were most dominant group (mean 47%) and composed largely of ANME‐2a which are characterized as anaerobic methane oxidizing archaea in broad environments. Furthermore Methanosaeta and Methanomicrobiales accounted for 23 and 29% of fragments, respectively, for all depths. Therefore, the presence of Methanomicrobiales and Methanosaeta in Pearl River estuarine sediments was indicative of both acetoclastic and hydrogenotrophic methanogenesis. In addition, the enrichments of methanogens also suggested the presence of acetoclastic and hydrogenotrophic methanogens in Pearl River estuarine sediments. This study is a significant step toward understanding methane cycling association of representative archaea in estuarine environments.
Potential of the salt‐tolerant laccase‐producing strain Trichoderma viride Pers. NFCCI‐2745 from an estuary in the bioremediation of phenol‐polluted environments
Authors: Divya L. M. , Prasanth G. K. , Sadasivan C.
Published: May 2013

Industrialization causes the generation of phenolic pollutants in the environment. The ability of laccases to oxidize phenolic compounds and reduce molecular oxygen to water has led to intensive studies on these enzymes. Although salt‐tolerant fungi are potential sources of enzymes for industrial applications, they have been inadequately explored for laccase production. This study describes the isolation of a salt‐ and phenol‐tolerant strain of Trichoderma sp. with the ability to produce laccase, and thus with the potential for industrial applications. The coconut husk retting ground in the estuaries of Kerala, India, a saline environment highly polluted with phenolic compounds, was selected for isolating the fungus. Enhanced laccase production was observed at 5–10 ppt salinity. The organism could grow even at 30 ppt salinity with reduced biomass production and laccase secretion. The optimum concentration of different phenolic compounds for enhanced laccase secretion ranged between 20 and 80 mg L−1. As the concentration of phenolic compounds increased beyond 200 mg L−1, the enzyme activity decreased and was completely inhibited at 800 mg L−1. The tolerance of Trichoderma viride Pers. NFCCI‐2745 to salinity and various phenolic compounds can be utilized in the bioremediation of highly saline and phenolic compound‐rich industrial effluents.
Molecular cloning and functional characterization of MnSOD from Dunaliella salina
Authors: Zhang Shu , Li Xin Ran , Xu Hui , Cao Yu , Ma Shu Han , Cao Yi , Qiao Dairong
Published: May 2013

Dunaliella salina, a unicellular green alga, has the potential to grow in hypersaline environments via one of its gene products, superoxide dismutase (SOD). The superoxide radicals (O2−) produced by environmental stresses can cause damage to cells, and SOD catalyzes the turnover of such free radicals to protect cells. In this study, the gene coding for SOD in D. salina was cloned and the product was further identified and characterized. The open reading frame of this gene was 651 bp long, encoding for 217 amino acids. According to the sequence alignment using BLAST, native polyacrylamide electrophoresis for SOD activity analysis, and atomic absorption spectroscopy analysis, this protein belongs to the manganese‐containing superoxide dismutase (MnSOD) family. Complementation analysis, performed by introducing plasmids carrying an inducible version of the D. salina gene encoding for MnSOD into an SOD‐deficient mutant of E.coli, revealed that this gene could not only complement the defects in SOD activity, but was also capable of providing a stronger tolerance to restrictive growth conditions, such as high salt and prolonged UV exposure, compared to the tolerance of wild‐type strains.
Inhibition by EGTA of the formation of a biofilm by clinical strains of Staphylococcus aureus
Authors: Liesse Iyamba J. M. , Seil M. , Nagant C. , Dulanto S. , Deplano A. , El Khattabi C. , Takaisi Kikuni N. B. , Dehaye J. P.
Published: May 2013

The effect of EGTA on the adhesion and on the formation of a biofilm by two reference and eight clinical strains of Staphylococcus aureus was studied. All the clinical strains were isolated from patients from Kinshasa. Spa typing confirmed that these clinical strains were distinct. The Biofilm Ring Test (BFRT®) showed that EGTA (100 µM–10 mM) inhibited the adhesion of the four clinical methicillin‐resistant (MRSA) strains and the crystal violet staining method that it inhibited the formation of a biofilm by all the strains. Divalent cations abolished the effect of EGTA on the formation of a biofilm, specially in the clinical MRSA strains. EGTA had no effect on established biofilms. Only concentrations of EGTA higher than 10 mM were toxic to eukaryotic cells. Our results establish the effectiveness and the safety of lock solutions with EGTA to prevent the formation in vitro of biofilms by S. aureus.
Removal of petroleum‐crude oil from aqueous solution by Saccharomyces cerevisiae SHSY strain necessitates at least an inducible CYP450ALK homolog gene
Authors: Hanano Abdulsamie , Al‐Arfi Malek , Shaban Mouhnad , Daher Amal , Shamma Motassim
Published: May 2013

Petroleum crude‐oil (PCO) components are known to be mutagenic or carcinogenic, and their contamination in soil and aquifer is of great environmental concern. PCO could be degraded by bacteria, fungi, and yeast. In yeast, the family CYP52 (P450ALKs) of Cytochrome P450 was described as n‐alkane‐degrading enzymes. In this study, we isolated a new strain SHSY of Saccharomyces able to grow on hydrocarbons compounds. Morphological and molecular characterization led to identify the isolated yeast SHSY as a Saccharomyces cerevisiae. SHSY strain had a remarkable ability to tolerate a high concentration of PCO and use it as a carbon source. A significant relationship was established between the increase in biomass (42.46 ± 1.01‐fold) and the disappearance of the crude oil (72.34%) in an aqueous solution. A 690‐bp amplicon corresponding to a high conserved region of known CYP450ALK genes was amplified in the genomic DNA of SHSY strain. The sequence of the amplified fragment shared a high identity (71.8%) with CYP52A3 gene of Pichia stipites. The expression of CYP52A3 homolog gene was induced and the expression of both InoP2/InoP4 transcription factor genes in SHSY was stimulated in the presence of PCO. The identified strain SHSY of S. cerevisiae presents an interesting model to minimize the mixed toxicity of PCO in polluted environmental sites.
Adaptation to tert‐butyl hydroperoxide at a plasma membrane level in the fission yeast Schizosaccharomyces pombe parental strain and its t‐BuOOH‐resistant mutant
Authors: Kálmán Nikoletta , Gazdag Zoltán , Čertík Milan , Belágyi József , Selim Samy A. , Pócsi István , Pesti Miklós
Published: May 2013

The one‐gene mutant hyd1‐190 of the fission yeast Schizosaccharomyces pombe displayed four‐fold resistance to tert‐butyl hydroperoxide (t‐BuOOH) in comparison with its parental strain hyd+. The cells of hyd1‐190 exhibited a quantitative alteration in the sterol content and hence in the fatty acid composition of the plasma membrane, reflected in a two‐fold amphotericin B sensitivity, increased rigidity of the plasma membrane, revealed by an elevated (Δ7.9 °C) phase‐transition temperature, measured by means of electron paramagnetic resonance spectroscopy, and a significantly decreased uptake of glycerol. Treatment of the strains with a subinhibitory concentration (0.2 mM) of t‐BuOOH induced adaptation via modification of the sterol and fatty acid compositions, resulting in increased (Δ3.95 °C) and decreased (Δ6.83 °C) phase‐transition temperatures of the hyd+ and hyd1‐190 strains, respectively, in order to defend the cells against the consequences of t‐BuOOH‐induced external oxidative stress. However, in contrast with hyd+, hyd1‐190 lacks the ability to adapt to t‐BuOOH at a cell level.
Identification and functional characteristics of chlorpyrifos‐degrading and plant growth promoting bacterium Acinetobacter calcoaceticus
Authors: Zhao Lei , Wang Fei , Zhao Jiao
Published: May 2013

A bacterial strain D10 with strong ability of degrading chlorpyrifos was isolated from rhizosphere of chives contaminated with pesticide. It was found that it's capable of utilizing chlorpyrifos as the sole source of carbon for growth, and within the first 4 days the extent of degradation at initial concentration of 100 mg L−1 was 60.0%. It also showed a high ability of degrading chlorpyrifos in sterilized soil, and the degradation reached up to 60.2% after 18 days. In addition, the strain D10 also showed multiple plant growth‐promoting traits of phosphate solubilization, indole‐3‐acetic acid and siderophore production. The results indicate that the strain D10 has potential in the application of pesticide‐degrading and plant growth promotion. Strain D10 was identified as Acinetobacter calcoaceticus based on its morphological, physiological‐biochemical properties and the 16S rRNA sequence analysis.
Halotolerant, acid‐alkali stable, chelator resistant and raw starch digesting α‐amylase from a marine bacterium Bacillus subtilis S8–18
Authors: Kalpana Balu Jancy , Pandian Shunmugiah Karutha
Published: May 2013

A halotolerant α‐amylase having the ability of digesting the insoluble raw starches was characterized from Bacillus subtilis S8–18, a marine sediment isolate from Palk Bay region. The electrophoresis techniques unveiled that the α‐amylase was indeed a monomer with a molecular weight of 57 kDa. The optimum temperature and pH for the enzyme activity were 60 °C and 6.0 respectively. The enzyme was highly stable for 24 h over a wide range of pH from 4.0 to 12.0 by showing 84–94% activity. Interestingly, by retaining 72% activity even after 24 h, the enzyme also showed tolerance towards 28% NaCl. The α‐amylase retained a minimum of 93% residual activity in 1 mM concentration for the selected divalent metal ions. The enzyme was found to be chelator resistant as it remained unaffected by 1 mM of EDTA and exhibited 96% activity even at 5 mM concentration. Furthermore, though 1% SDS caused remarkable reduction (68%) in amylase activity, the enzyme showed tolerance towards other detergents (1% of Triton‐X and Tween 80) with 85% activity. Additionally, the α‐amylase enzyme is capable of hydrolyzing the insoluble raw starch substrates which was evident from the scanning electron microscopic (SEM) and spectrophotometric analyses.
Outer membrane proteins of Fusobacterium necrophorum subsp. necrophorum and subsp. funduliforme
Authors: Kumar Amit , Peterson Greg , Nagaraja Tiruvoor G. , Narayanan Sanjeev
Published: May 2013

Fusobacterium necrophorum, classified into subsp. necrophorum (Fnn) and subsp. funduliforme (Fnf), is frequently associated with necrotic infections of animals and humans. The outer membrane proteins (OMP) of many Gram negative bacteria play an important role in bacterial adhesion and establishment of infection. The OMP profile of F. necrophorum has not been well characterized. We analyzed OMP of bovine strains of Fnn and Fnf and human strains of F. necrophorum. Electrophoretic separations of extracted OMP of Fnn and Fnf strains of cattle showed a total of 19 and 20 protein bands, respectively. The most prominent protein band was 40 kDa in Fnn and 37.5 kDa in Fnf. The four human clinical strains examined had more heterogeneous banding patterns and had different profiles than those of bovine Fnf strains. A total of 11 protein bands in Fnn and 13 protein bands in Fnf were recognized by sera from cattle with liver abscesses. The intensities of many of the bands in Fnn were higher than that of Fnf. We conclude that the two subspecies of F. necrophorum differ in their OMP profiles and the difference may account for differences in their virulence and involvement in the pathogenesis of necrotic infections.
Influence of sclerotia formation on ligninolytic enzyme production in Morchella crassipes
Authors: Kanwal Harpreet Kaur , Reddy M. Sudhakara
Published: May 2013

Morels are wild edible ascomycetous mushrooms that are highly prized because of their medicinal and nutritional qualities. Ligninolytic enzymes are considered as one of the most important enzymes in fungi due to their involvement in fruiting body formation during artificial cultivation on different substrates. In the life cycle of morels, sclerotia are the intermediate stage to form a fruiting body from mycelia. We have studied the production of ligninolytic enzymes by Morchella crassipes MR8 growing on different substrates and during sclerotia formation. This fungus is able to produce ligninolytic enzymes such as laccase (Lac), lignin peroxidase (LiP), and manganese‐dependent peroxidase (MnP) when grown on different substrates. Maximum Lac activity was observed when grown in wheat grains whereas maximum activities of MnP and LiP were observed when grown in rice straw. Laccase enzyme was produced in high titers during sclerotia formation and maturation when grown in combinations of soil and substrates. A large number of sclerotia was observed in soil and wheat grains, along with high titers of laccase. Cellulase activity was observed to be constant during sclerotia formation and maturation. The present study results suggest that laccase enzyme might play an important role in sclerotia formation in morels.
SecA2 is not required for secretion of the surface autolysin IspC in Listeria monocytogenes serotype 4b
Authors: Ronholm Jennifer , Zhang Cathy X.Y. , Cao Xudong , Lin Min
Published: May 2013

Listeria monocytogenes is one of several Gram‐positive bacteria known to contain an auxiliary ATPase (SecA2) involved in the Sec secretion of a subset of proteins important to bacterial pathogenesis, including autolysins. It is not known if IspC, a novel surface‐associated autolysin essential for full virulence of L. monocytogenes serotype 4b, is SecA2‐dependent for secretion. By creating a secA2 gene deletion (ΔsecA2) mutant from the wild type (WT) L. monocytogenes serotype 4b strain, in combination with the proteomic analysis of surface proteins and those secreted into the medium from both the mutant and the WT, we confirmed previous findings that two autolysins (p60 and NamA) are SecA2‐dependent for secretion. However, this approach did not identify IspC as one of the surface proteins affected by the SecA2 deletion. Further experiments with immunofluorescence microscopy and Western blotting indicated that IspC was well displayed on the surface of both the ΔsecA2 mutant and WT cells, while p60 was not, clearly indicating that the secretion of IspC is not attributed to the SecA2 pathway. This finding sets IspC apart from other autolysins involved in virulence, such as p60 and NamA, in that SecA2 is not required for IspC secretion.
Molecular characterization and lipase profiling of the yeasts isolated from environments contaminated with petroleum
Authors: Yalçın H. Tansel , Çorbacı Cengiz , Uçar Füsun B.
Published: May 2013

In the present study, 120 yeast isolates from different sources (active sludge, soil, and wastewater samples obtained from petroleum refinery and soil contaminated by petroleum) were obtained. The yeast isolates were screened for lipase production and twelve of the isolates (D3, D17, D24, D27, D30, D38, D40, D42, D44, D46, D56, and D57) exhibited lipase activity. Molecular characterization of the yeasts showing the lipase production was performed with RFLP of ITS1‐5.8S‐ITS2 and 18S rRNA and sequence analysis of D1/D2 domain of 26S rRNA. The 26S rRNA sequencing revealed that four new strains, D38, D40, D44 and D57 identified as Rhodotorula slooffiae, Candida davisiana, Cryptococcus diffluens, and Cryptococcus uzbekistanensis, respectively, are lipase producing yeast species. This study is the first report showed lipase production by these species. The other lipase producing strains identified as Candida parapsilosis (D3), Rhodotorula muciloginosa (D17 and D42), Cryptococcus albidus (D24, D27, D30, and D56), and Wickerhamomyces anomalus (D46).
Kinetic and thermodynamic characterization of lipase produced by Cellulomonas flavigena UNP3
Authors: Prajapati Vimal , Patel Honey , Trivedi Ujjval , Patel Kamlesh
Published: May 2013

Lipase of Cellulomonas flavigena UNP3 was purified by two‐step purification process comprising ammonium sulfate precipitation followed by gel permeation chromatography (GPC). The recovery of lipase after GPC was found to be 1.70% with 20.98‐fold increase in specific activity. The molecular weight of lipase protein was found to be 45.2 kDa by SDS–PAGE. Activation energy for p‐nitrophenol palmitate (pNPP) hydrolysis was 26.45 kJ mol−1, while temperature quotient (Q10) was found to be 1.64. The enzyme was found to be stable over wide pH range and thermally stable at 30–40 °C up to 60 min of incubation while exhibited maximum activity at 30 °C with pH 7.0. Vmax, Km, and Kcat for pNPP were found to be 666.71 U ml−1, 1.33 mM (pNPP) and 433 min−1, respectively. Activation energy for irreversible inactivation Ea(d) of lipase was 64.32 kJ mol−1. Thermodynamic parameters of irreversible inactivation of lipase and pNPP hydrolysis were also determined.
Regional frequency analysis and spatial pattern characterization of Dry Spells in Iran
Authors: Sarhadi Ali , Heydarizadeh Majid
Published: May 2013

This paper presents a methodology for regional frequency analysis and spatial pattern features of the Annual Maximum Dry Spell Length (AMDSL) as an indicator of drought conditions using the well‐known L‐moments approach and statistical‐based methods. Applying Ward's cluster‐analysis method identifies eight regions with distinctive AMDSL behaviours for Iran. Homogeneity testing indicates that most of these regions are homogenous. The goodness‐of‐fit test ZDist shows that Generalized Logistic; Generalized Extreme Value and Pearson type III, distributions fit best for most regions. The spatial pattern of L‐Moment statistics demonstrates that although the northwestern and northern parts of the country experience short dry spells, these periods are inconstant, and extreme dry spell events may happen in these areas. Almost all spatial mapping of AMDSLs at different probabilistic levels demonstrates that dry spells increase gradually from west to east and from north to south, and the southern parts (especially along the Persian Gulf and Oman Sea) and central areas, including most agricultural lands, stand out as the most sensitive to soil moisture deficits, because of longer lasting droughts. © 2013 Royal Meteorological Society
Contributing factors to adoption of electronic medical records in otolaryngology offices
Authors: Mahboubi Hossein , Salibian Ara A. , Wu Edward C. , Patel Madhukar S. , Armstrong William B.
Published: May 2013

Objectives/Hypothesis

(1) To determine the characteristics of outpatient otolaryngology offices with an electronic medical record (EMR) system, and (2) to compare those characteristics with the trends in surgical and medical specialties.

Study Design

Cross‐sectional analysis of U.S. representative data from the National Ambulatory Medical Care Survey (NAMCS).

Methods

The 2005 to 2010 NAMCS datasets were analyzed. Physicians' specialty was recoded as otolaryngology, all surgical specialties, and all specialties combined. Physician offices with all‐ or partial‐EMR system adoption were then compared to offices without EMR systems with respect to year; geographic region; urban setting; office setting; practice type; practice ownership; employment status; and revenues from Medicare, Medicaid, private insurance, and patient payment.

Results

Upon univariate analysis, EMR use was significantly higher among otolaryngology practices located in metropolitan areas and practices run or owned by larger groups of practitioners. Sources of patient revenue did not correlate with the likelihood of EMR use. Multivariate analysis revealed that EMR use by otolaryngologists was significantly associated with group practices and offices owned by institutions. Similar associations were observed with surgical specialties combined in addition to a higher EMR usage in practices with more than 25% of total revenue from private insurance.

Conclusions

EMR utilization by otolaryngology practices appears similar to that of other specialties, and is more likely in metropolitan areas and larger practice settings. Despite the announcement of incentive programs under Medicare and Medicaid in 2009, EMR usage was not dependent on the percentage of physicians' total revenue from these sources.

Level of Evidence

N/A. Laryngoscope, 123:2658–2663, 2013
Factors affecting time to revision sinus surgery for nasal polyps: A 25‐year experience
Authors: Wu Arthur W. , Ting Jonathan Y. , Platt Michael P. , Tierney Hien T. , Metson Ralph
Published: May 2013

Objectives/Hypothesis

Surgical treatment for chronic rhinosinusitis with nasal polyps (CRSwNP) is often followed by polyp regrowth with return of symptoms. The purpose of this study is to identify clinical factors that influence the time interval to revision sinus surgery in patients with nasal polyps.

Study Design

Retrospective cohort study.

Methods

Records of 299 individuals who underwent two or more surgeries for the diagnosis of nasal polyps by the senior author (RM) from 1987 through 2011 were reviewed. The time between surgical interventions were compared to patient demographics, comorbidities, endoscopic examination, computed tomography (CT) stage, extent of surgery, and pathologic findings.

Results

The mean time interval between polyp surgeries was 4.87 ± 3.61 years (range 0.7–18.6 years). The median time to revision surgery was shorter in patients who smoked compared to nonsmokers (2.82 vs. 4.31 years, respectively, P = .022) and longer in patients who underwent middle turbinate resection rather than preservation (4.56 vs. 3.93 years, respectively, P = .048). Kaplan‐Meier survival analysis confirmed these findings, but the beneficial effect of turbinectomy appeared to dissipate by 8 years. Neither a history of asthma nor advanced CT stage influenced the time to revision surgery.

Conclusion

The time course between sinus surgeries in patients with regrowth of nasal polyps appears to be affected by certain modifiable extrinsic factors, including smoking on the part of the patient and operative technique on the part of the surgeon. The performance of middle turbinate resection during sinus surgery appears to extend the time interval until a revision procedure is required.

Level of Evidence

2b. Laryngoscope, 124:29–33, 2014
The Utilization of Isolation Chromophore in an “A3+B2” Type Second‐Order Nonlinear Optical Hyperbranched Polymer
Authors: Wu Wenbo , Ye Cheng , Qin Jingui , Li Zhen
Published: May 2013

In this paper, a new nonlinear optical (NLO) hyperbranched polymer P1 is designed and synthesized successfully through one‐pot “A3+B2” approach via a simple Sonogashira coupling reaction, in which isolation chromophore is introduced to improve its comprehensive performance such as NLO activity, optical transparency, and stability. For comparison, its analogs, P2 and P3, just containing one type of chromophore, are also prepared. Although P1 cannot be well poled under our test conditions, its NLO coefficient is still much higher than its analogs P2, P3, and the linear polyaryleneethynylene P4, which also contains isolation chromophore, indicating the advantages of isolation chromophore and the three‐dimensional (3D) spatial isolation from the highly branched structure in the NLO field.

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Chiral Amplification during Asymmetric‐Induced Copolymerization of Phenylacetylenes with Tight Cis‐Cisoidal Main Chains
Authors: Liu Lijia , Mottate Kazuomi , Zhang Geng , Aoki Toshiki , Kaneko Takashi , Teraguchi Masahiro
Published: May 2013

A novel phenylacetylene (1) having two hydroxyl groups and a chiral pinanyl group together with the other three related phenylacetylenes has been synthesized and (co)polymerized by using an achiral catalytic system. Among the four monomers, only 1 is suitable to the asymmetric‐induced polymerization (AIP). Chiral amplification phenomenon is only observed in the copolymerization of 1 with an achiral phenylacetylene having two hydroxyl groups (3). The tight helical cis‐cisoidal main chain formed by making intramolecular hydrogen bonds between the hydroxyl groups in the copoly(1/3) enhances the efficiency of chiral induction and as a result chiral amplification phenomenon is observed during the copolymerization.

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Diffusion‐weighted MRI and its role in prostate cancer
Authors: Tamada Tsutomu , Sone Teruki , Jo Yoshimasa , Yamamoto Akira , Ito Katsuyoshi
Published: May 2013

In the last 5 years, the multiparametric approach has been investigated as the method for the MRI of prostate cancer. In multiparametric MRI of the prostate, at least two functional MRI techniques, such as diffusion‐weighted MRI (DW‐MRI) and dynamic contrast‐enhanced MRI, are combined with conventional MRI, such as T2‐weighted imaging. DW‐MRI has the ability to qualitatively and quantitatively represent the diffusion of water molecules by the apparent diffusion coefficient, which indirectly reflects tissue cellularity. DW‐MRI is characterized by a short acquisition time without the administration of contrast medium. Thus, DW‐MRI has the potential to become established as a noninvasive diagnostic method for tumor detection and localization, tumor aggressiveness, local staging and local recurrence after various therapies. Accordingly, radiologists should recognize the principles of DW‐MRI, the methods of image acquisition and the pitfalls of image interpretation. Copyright © 2013 John Wiley & Sons, Ltd.
An approximate method for solving a class of nonlinear optimal control problems
Authors: Saberi Nik H. , Effati S.
Published: May 2013

This paper presents a novel computational approach to generate the suboptimal solutions for a class of nonlinear optimal control problems (OCP's) with a quadratic performance index. Our method is based on the one‐dimensional differential transform method (DTM) and new polynomials that are called DT's polynomials. This method simplifies the difficulties and massive computational work for calculating the differential transform of nonlinear function. The convergence of proposed method are discussed in detail. This method consists of a new modified version of the DTM together with a shooting method such as procedure, for solving the extreme conditions obtained from the Pontryagin's maximum principle. The results reveal that the proposed methods are very effective and simple. Comparisons are made between new DTM generated results, results from literature, andMATLABbvp4cgenerated results, and good agreement is observed. Copyright © 2013 John Wiley & Sons, Ltd.
Southwest Pacific Ocean response to a warming world: Using Mg/Ca, Zn/Ca, and Mn/Ca in foraminifera to track surface ocean water masses during the last deglaciation
Authors: Marr Julene P. , Carter Lionel , Bostock Helen C. , Bolton Annette , Smith Euan
Published: May 2013

In situ measurements of Mg/Ca, Zn/Ca, Mn/Ca, and Ba/Ca in Globigerinoides bulloides and Globigerina ruber from southwest Pacific core top sites and plankton tow are reported and their potential as paleoproxies is explored. The modern samples cover 20° of latitude from 34°S to 54°S, 7–19°C water temperature, and variable influence of subantarctic (SAW) and subtropical (STW) surface waters. Trace element signatures recorded in core top and plankton tow planktic foraminifera are examined in the context of the chemistry and nutrient profiles of their modern water masses. Our observations suggest that Zn/Ca and Mn/Ca may have the potential to trace SAW and STW. Intraspecies and interspecies offsets identified by in situ measurements of Mg/Ca and Zn/Ca indicate that these ratios may also record changes in thermal and nutrient stratification in the upper ocean. We apply these potential proxies to fossilized foraminifera from the high‐resolution core MD97 2121. At the Last Glacial Maximum, surface water Mg/Ca temperature estimates indicate that temperatures were approximately 6–7°C lower than those of the present, accompanied by low levels of Mn/Ca and Zn/Ca and minimal thermal and nutrient stratification. This is consistent with regional dominance of SAW and reduced STW inflow associated with a reduced South Pacific Gyre (SPG). Upper ocean thermal and nutrient stratification collapsed during the Antarctic Cold Reversal, before poleward migration of the zonal winds and ocean fronts invigorated the SPG and increased STW inflow in the early Holocene. Together with reduced winds, this favored a stratified upper ocean from circa 10 ka to the present.
Interstitial 4q deletion associated with a mosaic complementary supernumerary marker chromosome in prenatal diagnosis
Authors: Capalbo Anna , Sinibaldi Lorenzo , Bernardini Laura , Spasari Iolanda , Mancuso Brunella , Maggi Eugenio , Novelli Antonio
Published: May 2013

What's already known about this topic?

Chromosomal deletion associated with a complementary ring is a very rare cytogenetic finding. Genetic counselling in prenatally ascertained cases without ultrasound defects is extremely complex because this rearrangement has been associated both to normal and abnormal phenotype.

What does this study add?

This case elucidates the importance of the integrated approach by microarray‐based and standard cytogenetics analysis to accurately characterize chromosome rearrangements. It prompted to review all the reported cases of proximal 4q deletion to refine the karyotype/phenotype correlation.
Rivaroxaban: Practical Considerations for Ensuring Safety and Efficacy
Authors: Smythe Maureen A. , Fanikos John , Gulseth Michael P. , Wittkowsky Ann K. , Spinler Sarah A. , Dager William E. , Nutescu Edith A.
Published: May 2013

Rivaroxaban is the first agent available within a new class of anticoagulants called direct factor Xa inhibitors. Rivaroxaban is approved for use in the United States for the prevention of stroke and systemic embolism in patients with nonvalvular atrial fibrillation, for the prevention of deep vein thrombosis in patients undergoing total hip replacement and total knee replacement, for the treatment of deep vein thrombosis and pulmonary embolism, and for the reduction in risk of recurrence of deep vein thrombosis and pulmonary embolism (with additional indications under review). Rivaroxaban dose and frequency of administration vary depending on the indication. As of result of predictable pharmacokinetics and pharmacodynamics, a fixed dose of rivaroxaban is administered without routine coagulation testing. Rivaroxaban has a short half‐life, undergoes a dual mode of elimination (hepatic and renal), and is a substrate for P‐glycoprotein. Rivaroxaban has a lower potential for drug interactions compared with warfarin. Despite the advantages of a once/day fixed‐dose oral agent, in many clinical situations limited evidence is available to guide optimal management of rivaroxaban therapy. In this article, we review the available evidence and provide recommendations where possible for such situations including the desire to monitor the anticoagulation intensity, use in special patient populations, managing drug interactions, and transitioning across anticoagulant agents. Potential strategies for reversing rivaroxaban's anticoagulant effect are reviewed. Health systems will need to perform a systematic safety evaluation and ensure that numerous hospital policies related to anticoagulation are updated to include rivaroxaban. A comprehensive approach to education is needed for clinicians, patients, and technical support personnel involved in patient interactions to ensure safe use.
Shotgun proteomic analysis of sarcoplasmic reticulum preparations from rabbit skeletal muscle
Authors: Liu Zhouying , Du Xiangning , Yin Changcheng , Chang Zhenzhan
Published: May 2013

To obtain a comprehensive understanding of proteins involved in excitation–contraction coupling, a catalog of proteins from sarcoplasmic reticulum (SR) membrane fractions of New Zealand white rabbit skeletal muscle was analyzed by an optimized shotgun proteomic method. Light and heavy SR membrane fractions were obtained by nonlinear sucrose gradient centrifugation and separated by 1DE followed by a highly reproducible, automated LC‐MS/MS on the hybrid linear ion trap (LTQ) Orbitrap mass spectrometer. By integrating as low as 1% false discovery rate as one of the features for quality control method, 483 proteins were identified from both of the two independent SR preparations. Proteins involved in calcium release unit complex, including ryanodine receptor 1, dihydropyridine receptor, calmodulin, triadin, junctin, and calsequestrin, were all detected, which offered validation for this protein identification method. Rigorous bioinformatics analysis was performed. Protein pI value, molecular weight range, hydrophobicity index, and transmembrane region were calculated using bioinformatics softwares. Eighty‐three proteins were classified as hydrophobic proteins and 175 proteins were recognized as membrane proteins. Based on the proteomic analysis results, we found as the first time that not only transverse tubule but also mitochondrion physically connected to SR. The complete mapping of these proteomes may help in the elucidation of the process of excitation–contraction coupling and excitation–metabolism coupling.
Protein profile of Lupinus texensis phloem sap exudates: Searching for Fe‐ and Zn‐containing proteins
Authors: Lattanzio Giuseppe , Andaluz Sofía , Matros Andrea , Calvete Juan José , Kehr Julia , Abadía Anunciación , Abadía Javier , López‐Millán Ana‐Flor
Published: May 2013

The aim of this study was to obtain a comprehensive overview of the phloem sap protein profile of Lupinus texensis, with a special focus on proteins binding Fe and Zn. L. texensis was chosen as model plant given the simplicity to obtain exudates from sieve elements. Protein profiling by 2DE revealed 249 spots, and 54 of them were unambiguously identified by MALDI‐MS and ESI‐MS/MS. The largest number of identified protein species belongs to protein modification/turnover and general metabolism (19–21%), followed by redox homeostasis (9%) and defense and cell structural components (7%). This protein profile is similar to that reported in other plant species, suggesting that the phloem sap proteome is quite conserved. Staining of 2DE gels for Fe‐containing proteins and affinity chromatography experiments revealed the presence of two low molecular weight Fe‐binding proteins in phloem sap: a metallothionein‐like protein type 2B identified in the Fe‐affinity chromatography, and a second protein identified with both Fe staining methods. This protein species had a molecular weight of 13.5 kDa, a pI of 5.6 and 51% homology to a phloem‐specific protein from Medicago truncatula. Zinc affinity chromatography revealed four Zn‐binding proteins in phloem sap, one belonging to the dehydrin family and three Zn finger proteins.
Proteomic profiling of cardiomyopathic tissue from the aged mdx model of Duchenne muscular dystrophy reveals a drastic decrease in laminin, nidogen and annexin
Authors: Holland Ashling , Dowling Paul , Zweyer Margit , Swandulla Dieter , Henry Michael , Clynes Martin , Ohlendieck Kay
Published: May 2013

The majority of patients afflicted with Duchenne muscular dystrophy develop cardiomyopathic complications, warranting large‐scale proteomic studies of global cardiac changes for the identification of new protein markers of dystrophinopathy. The aged heart from the X‐linked dystrophic mdx mouse has been shown to exhibit distinct pathological aspects of cardiomyopathy. In order to establish age‐related alterations in the proteome of dystrophin‐deficient hearts, cardiomyopathic tissue from young versus aged mdx mice was examined by label‐free LC‐MS/MS. Significant age‐dependent alterations were established for 67 proteins, of which 28 proteins were shown to exhibit a lower abundance and 39 proteins were found to be increased in their expression levels. Drastic changes were demonstrated for 17 proteins, including increases in Ig chains and transferrin, and drastic decreases in laminin, nidogen and annexin. An immunblotting survey of young and old wild‐type versus mdx hearts confirmed these proteomic findings and illustrated the effects of natural aging versus dystrophin deficiency. These proteome‐wide alterations suggest a disintegration of the basal lamina structure and cytoskeletal network in dystrophin‐deficient cardiac fibres, increased levels of antibodies in a potential autoimmune reaction of the degenerating heart, compensatory binding of excess iron and a general perturbation of metabolic pathways in dystrophy‐associated cardiomyopathy.
PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post‐translational modifications
Authors: Nanni Paolo , Panse Christian , Gehrig Peter , Mueller Susanne , Grossmann Jonas , Schlapbach Ralph
Published: May 2013

Mass spectrometry (MS) analysis of peptides carrying post‐translational modifications is challenging due to the instability of some modifications during MS analysis. However, glycopeptides as well as acetylated, methylated and other modified peptides release specific fragment ions during CID (collision‐induced dissociation) and HCD (higher energy collisional dissociation) fragmentation. These fragment ions can be used to validate the presence of the PTM on the peptide. Here, we present PTM MarkerFinder, a software tool that takes advantage of such marker ions. PTM MarkerFinder screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, it reports and annotates the HCD and the corresponding electron transfer dissociation (ETD) spectrum (when present), and summarizes information on the type, number, and ratios of marker ions found in the data set. In the present work, a sample containing enriched N‐acetylhexosamine (HexNAc) glycopeptides from yeast has been analyzed by liquid chromatography‐mass spectrometry on an LTQ Orbitrap Velos using both HCD and ETD fragmentation techniques. The identification result (Mascot .dat file) was submitted as input to PTM MarkerFinder and screened for HexNAc oxonium ions. The software output has been used for high‐throughput validation of the identification results.
Anxiety, depression and defense mechanisms associated with treatment decisional preferences and quality of life in non‐metastatic breast cancer: a 1‐year prospective study
Authors: Hyphantis Thomas , Almyroudi Augoustina , Paika Vassiliki , Degner Lesley F. , Carvalho André F. , Pavlidis Nicholas
Published: May 2013

Objective

Treatment decisional preferences impact breast cancer patients' health‐related quality of life (HRQoL) and may relate to psychological variables, although many aspects of this relationship remain unknown. This prospective study aimed to assess psychological correlates of treatment decisional preferences and predictors of HRQoL in women with early non‐metastatic breast cancer.

Methods

Of the 124 women initially assessed for anxiety (Spielberger's State–Trait Anxiety Inventory) and depressive (Center for Epidemiologic Studies‐Depression (CES‐D)) symptoms, HRQoL (WHOQOL‐BREF), and defense mechanisms (Life Style Index), 82 (66.1%) completed the 1‐year follow‐up. Mean age was 54.6 years (SD = 9.76), and mean disease duration was 19.4 months (SD = 25.55); 19.5% had stage I, 63.4% stage II and 17.1% stage III disease. The predictive power and moderator effects of psychological variables were tested using multiple and hierarchical regression models.

Results

Depressive symptoms and physical HRQoL improved significantly, state anxiety and mental and environment HRQoL remained stable, and social relations HRQoL deteriorated over the 1‐year period. Older age (p = 0.021) and higher scores in repression defense (p = 0.044) were independently associated with passive decisional preferences. Earlier stage of cancer (p = 0.043), lower state anxiety (p = 0.039), lower repression scores (p = 0.021) and improvement in depressive symptoms (p < 0.001) predicted physical HRQoL improvement. Moderation analysis showed that active decisional preferences predicted physical HRQoL improvement, but only in those women with lower repression levels.

Conclusions

Defense mechanisms are associated with treatment decisional preferences and interact with factors predicting HRQoL in women with breast cancer. Clinicians should address the patients' anxiety and depressive symptoms and refer patients with high repression tendencies for psychological evaluation and management. Copyright © 2013 John Wiley & Sons, Ltd.
Multipotent stromal cells induce human regulatory T cells through a novel pathway involving skewing of monocytes toward anti-inflammatory macrophages
Authors: Melief Sara M. , Schrama Ellen , Brugman Martijn H. , Tiemessen Machteld M. , Hoogduijn Martin J. , Fibbe Willem E. , Roelofs Helene
Published: May 2013

Multipotent stromal cells (MSC) have been shown to possess immunomodulatory capacities and are therefore explored as a novel cellular therapy. One of the mechanisms through which MSC modulate immune responses is by the promotion of regulatory T cell (Treg) formation. In this study, we focused on the cellular interactions and secreted factors that are essential in this process. Using an in vitro culture system, we showed that culture-expanded bone marrow-derived MSC promote the generation of CD4+CD25hiFoxP3+ T cells in human PBMC populations and that these populations are functionally suppressive. Similar results were obtained with MSC-conditioned medium, indicating that this process is dependent on soluble factors secreted by the MSC. Antibody neutralization studies showed that TGF-β1 mediates induction of Tregs. TGF-β1 is constitutively secreted by MSC, suggesting that the MSC-induced generation of Tregs by TGF-β1 was independent of the interaction between MSC and PBMC. Monocyte-depletion studies showed that monocytes are indispensable for MSC-induced Treg formation. MSC promote the survival of monocytes and induce differentiation toward macrophage type 2 cells that express CD206 and CD163 and secrete high levels of IL-10 and CCL-18, which is mediated by as yet unidentified MSC-derived soluble factors. CCL18 proved to be responsible for the observed Treg induction. These data indicate that MSC promote the generation of Tregs. Both the direct pathway through the constitutive production of TGF-β1 and the indirect novel pathway involving the differentiation of monocytes toward CCL18 producing type 2 macrophages are essential for the generation of Tregs induced by MSC.
Regulation of Trachebronchial Tissue-Specific Stem Cell Pool Size
Authors: Ghosh Moumita , Smith Russell W. , Runkle Christine M. , Hicks Douglas A. , Helm Karen M. , Reynolds Susan D.
Published: May 2013

Tissue-specific stem cell (TSC) number is tightly regulated in normal individuals but can change following severe injury. We previously showed that tracheobronchial epithelial TSC number increased after severe naphthalene (NA) injury and then returned to normal. This study focused on the fate of the supernumerary TSC and the signals that regulate TSC pool size. We used the Keratin 5-rTA/Histone 2B:green fluorescent protein (GFP) model to purify basal cells that proliferated infrequently (GFPbright) or frequently (GFPdim) after NA injury. Both populations contained TSC but TSCs were 8.5-fold more abundant in the GFPbright population. Interestingly, both populations also contained a unipotential basal progenitor (UPB), a mitotic basal cell subtype whose daughters were terminally differentiated basal cells. The ratio of TSC to UPB was 5:1 in the GFPbright population and 1:5 in the GFPdim population. These data suggested that TSC proliferation in vivo promoted TSC-to-UPB differentiation. To evaluate this question, we cloned TSC from the GFPbright and GFPdim populations and passaged the clones seven times. We found that TSC number decreased and UPB number increased at each passage. Reciprocal changes in TSC and UPB frequency were more dramatic in the GFPdim lineage. Gene expression analysis showed that β-catenin and Notch pathway genes were differentially expressed in freshly isolated TSC derived from GFPbright and GFPdim populations. We conclude that (a) TSC and UPB are members of a single lineage; (b) TSC proliferation in vivo or in vitro promotes TSC-to-UPB differentiation; and (c) an interaction between the β-catenin and Notch pathways regulates the TSC-to-UPB differentiation process. Stem Cells  2013;31:2767–2778
Multi-centered first order formalism
Authors: Ferrara Sergio , Marrani Alessio , Shcherbakov Andrey , Yeranyan Armen
Published: May 2013

Abstract

We propose a first order formalism for multi-centered black holes with flat three-dimensional base-space, within the stu model of N = 2, D = 4 ungauged MaxwellEinstein supergravity. This provides a unified description of first order flows of this universal sector of all models with a symmetric scalar manifold which can be obtained by dimensional reduction from five dimensions.

We develop a D = 3 Cartesian formalism which suitably extends the definition of central and matter charges, as well as of black hole effective potential and first order “fake” superpotential, in order to deal with not necessarily axisimmetric solutions, and thus with multi-centered and/or (under-)rotating extremal black holes.

We derive general first order flow equations for composite non-BPS and almost BPS classes, and we analyze some of their solutions, retrieving various single-centered (static or under-rotating) and multi-centered known systems.

As in the t
3 model, the almost BPS class turns out to split into two general branches, and the well known almost BPS system is shown to be a particular solution of the second branch.