bluuebunny/crossref_metadata_2025 huggingface dataset:
QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis
Authors: van der Kamp Marc W. , Chaudret Robin , Mulholland Adrian J.
Published: January 2013

Ketosteroid isomerase (Δ5–3–keto steroid isomerase or steroid Δ–isomerase) is a highly efficient enzyme at the centre of current debates on enzyme catalysis. We have modelled the reaction mechanism of the isomerization of 3–oxo‐Δ5–steroids into their Δ4‐conjugated isomers using high‐level combined quantum mechanics/molecular mechanics (QM/MM) methods, and semi‐empirical QM/MM molecular dynamics simulations. Energy profiles were obtained at various levels of QM theory (AM1, B3LYP and SCS–MP2). The high‐level QM/MM profile is consistent with experimental data. QM/MM dynamics simulations indicate that active site closure and desolvation of the catalytic Asp38 occur before or during formation of dienolate intermediates. These changes have a significant effect on the reaction barrier. A low barrier to reaction is found only when the active site is closed, poising it for catalysis. This conformational change is thus integral to the whole process. The effects on the barrier are apparently largely due to changes in solvation. The combination of high‐level QM/MM energy profiles and QM/MM dynamics simulation shows that the reaction involves active site closure, desolvation of the catalytic base, efficient isomerization and re‐opening of the active site. These changes highlight the transition between the ligand binding/releasing form and the catalytic form of the enzyme. The results demonstrate that electrostatic interactions (as a consequence of pre‐organization of the active site) are crucial for stabilization during the chemical reaction step, but closure of the active site is essential for efficient catalysis to occur.
Soil carbon changes under Miscanthus driven by C4 accumulation and C3 decompostion – toward a default sequestration function
Authors: Poeplau Christopher , Don Axel
Published: January 2013

Bioenergy has to meet increasing sustainability criteria in the EU putting conventional bioenergy crops under pressure. Alternatively, perennial bioenergy crops, such as Miscanthus, show higher greenhouse gas savings with similarly high energy yields. In addition, Miscanthus plantations may sequester additional soil organic carbon (SOC) to mitigate climate change. As the land‐use change in cropland to Miscanthus involves a C3‐C4 vegetation change (VC), it is possible to determine the dynamic of Miscanthus‐derived SOC (C4 carbon) and of the old SOC (C3 carbon) by the isotopic ratio of 13C to 12C. We sampled six croplands and adjacent Miscanthus plantations exceeding the age of 10 years across Europe. We found a mean C4 carbon sequestration rate of 0.78 ± 0.19 Mg ha−1 yr−1, which increased with mean annual temperature. At three of six sites, we found a significant increase in C3 carbon due to the application of organic fertilizers or difference in baseline SOC, which we define as non‐VC‐induced SOC changes. The Rothamsted Carbon Model was used to disentangle the decomposition of old C3 carbon and the non‐VC‐induced C3 carbon changes. Subsequently, this method was applied to eight more sites from the literature, resulting in a climate‐dependent VC‐induced SOC sequestration rate (0.40 ± 0.20 Mg ha−1 yr−1), as a step toward a default SOC change function for Miscanthus plantations on former croplands in Europe. Furthermore, we conducted a SOC fractionation to assess qualitative SOC changes and the incorporation of C4 carbon into the soil. Sixteen years after Miscanthus establishment, 68% of the particulate organic matter (POM) was Miscanthus‐derived in 0–10 cm depth. POM was thus the fastest cycling SOC fraction with a C4 carbon accumulation rate of 0.33 ± 0.05 Mg ha−1 yr−1. Miscanthus‐derived SOC also entered the NaOCl‐resistant fraction, comprising 12% in 0–10 cm, which indicates that this fraction was not an inert SOC pool.
Mineral soil carbon fluxes in forests and implications for carbon balance assessments
Authors: Buchholz Thomas , Friedland Andrew J. , Hornig Claire E. , Keeton William S. , Zanchi Giuliana , Nunery Jared
Published: January 2013

Forest carbon cycles play an important role in efforts to understand and mitigate climate change. Large amounts of carbon (C) are stored in deep mineral forest soils, but are often not considered in accounting for globalCfluxes because mineral soilCis commonly thought to be relatively stable. We exploreCfluxes associated with forest management practices by examining existing data on forestCfluxes in the northeasternUS. Our findings demonstrate that mineral soilCcan play an important role inCemissions, especially when considering intensive forest management practices. Such practices are known to cause a high abovegroundCflux to the atmosphere, but there is evidence that they can also promote comparably high and long‐term belowgroundCfluxes. If these additional fluxes are widespread in forests, recommendations for increased reliance on forest biomass may need to be reevaluated. Furthermore, existing protocols for the monitoring of forestCoften ignore mineral soilCdue to lack of data. ForestCanalyses will be incomplete until this problem is resolved.
Nitrogen fertilization to optimize the greenhouse gas balance of hemp crops grown for biomass
Authors: Finnan John , Burke Brendan
Published: January 2013

Nitrogen trials were carried out on hemp crops grown in Ireland over a 3 year period to identify nitrogen fertilization strategies which optimize the greenhouse gas (GHG) and energy balances of hemp crops grown for biomass. Nitrogen rates up to 150 kg N ha−1 were used in the study. Yield increased with nitrogen rate up to 120 kg N ha−1 for early (Ferimon), mid (Felina 32) and late maturing (Futura 75) varieties. Variety had a significant effect on yield with yields increasing with maturation date. In 2 years of the study, certain application rates of nitrogen were applied either at sowing, at emergence, after emergence or split between these dates to determine if nitrogen rates could be reduced by delaying or splitting the applications. The application of nitrogen at times later than sowing or in splits during the early part of the growing season had no significant effect on biomass yield compared with the practice of applying nitrogen at the time of sowing. Late applications of nitrogen reduced leaf chlorophyll content and height early in the growing season. Later in the growing season, there was no difference in height between treatments although the highest concentrations of chlorophyll were found in the leaves of the late application treatment. Nitrogen rate and the timing of nitrogen application had no effect on plant density. Biomass yield, net energy and net GHG mitigation increased up to an application rate of 120 kg N ha−1, this result was independent of soil type or soil nitrogen level. Net GHG and energy balance of hemp crops grown for biomass are optimized if late maturing varieties are used for biomass production and a nitrogen rate of 120 kg ha−1 is applied at sowing.
Do the elevational limits of deciduous tree species match their thermal latitudinal limits?
Authors: Randin Christophe F. , Paulsen Jens , Vitasse Yann , Kollas Chris , Wohlgemuth Thomas , Zimmermann Niklaus E. , Körner Christian
Published: January 2013

Aim

We compared the upper limits of 18 deciduous tree species with respect to elevation in Switzerland and latitude in Europe. We hypothesized that species would exhibit the same relative positions along elevation and latitude, which can be expected if species have reached their thermal cold limit along both gradients.

Location

Europe and Switzerland.

Methods

We developed a method to identify a least biased estimate of the elevational and latitudinal cold temperature limits of species and for comparing the relative rank positions with respect to these two limits. We applied an algorithm to calculate the elevation of the potential tree line for each point in the gridded landscape of Europe and Switzerland. For each occurrence of each species, the elevation was extracted from digital elevation models. The vertical distance between the elevation of the potential regional climatic tree line and the uppermost species occurrences was calculated and used for comparisons between elevation and latitude.

Results

We found a strong relationship between the thermal latitudinal and elevational distances of species’ cold limits to the potential tree line, with only marginally significantly different rank positions (P = 0.057) detected along elevational and latitudinal gradients. A first group of nine species showed very similar thermal distances to the potential tree lines along elevation and latitude. Among these species, eight showed a significant decrease in their elevational limit towards high latitudes across mountainous regions of Europe. A second group of seven species occupied a climatic niche closer to the tree line at the edge of their latitudinal range, and only two species did not fill their thermal niche.

Main conclusions

Our study provides support for the common concept of a species range–environment equilibrium. Notably, we did not detect a stronger deviation for the filling of thermal niches at latitudinal limits compared with elevational limits, although the former involves a species covering a much greater geographic distance.
Large‐scale geographic patterns of diversity and community structure of pelagic crustacean zooplankton in Canadian lakes
Authors: Pinel‐Alloul Bernadette , André Adrien , Legendre Pierre , Cardille Jeffrey A. , Patalas Kasimierz , Salki Alex
Published: January 2013

Aim

We tested the energy and metabolic theories for explaining diversity patterns of crustacean zooplankton in Canadian lakes, and evaluated the influence of regional and local environments on community structure.

Location

The 1665 studied lakes are distributed across Canada in 47 ecoprovinces.

Methods

Our database included the occurrence of 83 pelagic crustacean species. The regional species richness in each ecoprovince was estimated using the average local species richness per lake and the first‐order jackknife diversity index. Using a principal component plot and forward selection in a multiple regression we identified the most important predictors of regional species richness estimates. We tested the predictions of the species richness‐energy hypothesis using climatic variables at regional scale, and of the metabolic theory using the inverse of air temperature. To evaluate the influence of regional and local environmental drivers, we carried out a redundancy analysis between crustacean species occurrences and regional climate and lake environmental factors on a subset of 458 lakes.

Results

Estimates of pelagic crustacean species richness in Canadian ecoprovinces varied from 3 to 10 species per lake (average local species richness) or 8 to 52 species per ecoprovince (Jackknife diversity index). Our study fully supports the species richness‐energy hypothesis and partially the metabolic theory. Mean daily global solar radiation was the most important regional predictor, explaining 51% of the variation in the regional species richness among ecoprovinces. Together, regional climate and local lake environment accounted for 31% of the total variation in community structure. Regional‐scale energy variables accounted for 24% of the total explained variation, whereas local‐scale lake conditions had less influence (2%).

Main conclusions

The richness‐energy theory explains diversity patterns of freshwater crustacean zooplankton in Canadian ecoprovinces. Solar radiation is the best predictor explaining regional species richness in ecoprovinces and community structure of pelagic crustaceans in Canadian lakes.
Mechanisms underlying global temperature‐related patterns in leaf longevity
Authors: Kikuzawa Kihachiro , Onoda Yusuke , Wright Ian J. , Reich Peter B.
Published: January 2013

Aim

At a global scale, the relationship of leaf longevity (LL) to mean annual temperature (MAT) is positive for deciduous species but negative for evergreen species. The aim of this paper is to understand the mechanisms underlying these contrasting patterns of leaf longevity, from a cost–benefit perspective.

Location

Global.

Methods

We tested our hypothesis that contrasting LL–MAT relationships in evergreen and deciduous species result from differing adaptations to variation in the length of the annual favourable period. We defined f as the portion of the year when monthly temperature and water availability were favourable. We examined whether the contrasting LL patterns with MAT can be also seen with f. Next, we calculated the optimal LL that maximizes carbon gain per unit time across a range of f.

Results

The contrasting LL patterns across MAT were also found across f. Our optimization model successfully reproduced the contrasting LL patterns across f for the evergreen (LL longer than 1 year) and deciduous plants. The model shows that longer LL is required to maximize carbon gain for evergreen plants in shorter f, while LL of deciduous plants decreases with decreasing f. Without any a priori trait association, the model reproduced the well‐known LL–leaf mass per area (LMA) relationship. The model also reproduced observed shifts in LL–LMA relationships across MAT or f. Evergreen leaves in long f need greater LMA to maintain LL than those in shorter f.

Main conclusions

Observed contrasting LL–MAT patterns in deciduous and evergreen species can be reproduced via the simple rule of maximizing carbon gain across different lengths of favourable periods. Our model provides a mechanistic explanation for the empirical global patterns of several key leaf traits and their relationships.
Role of SMG‐1‐mediated Upf1 phosphorylation in mammalian nonsense‐mediated mRNA decay
Authors: Yamashita Akio
Published: January 2013

SMG‐1, a member of the PIKK (phosphoinositide 3‐kinase‐related kinase) family, plays a critical role in the mRNA quality control system known as nonsense‐mediated mRNA decay (NMD). NMD protects cells from the accumulation of aberrant mRNAs with premature termination codons (PTCs) which encode nonfunctional or potentially harmful truncated proteins. SMG‐1 directly phosphorylates Upf1 helicase, another key component of NMD, upon recognition of PTC on postspliced mRNA during the initial round of translation. Phosphorylated‐Upf1 recruits the SMG‐5/SMG‐7 complex to induce ribosome dissociation and decapping‐mediated decay. Phospho‐Upf1 also recruits the SMG‐6 endonuclease which might be involved in endo‐cleavage. Upf1 ATPase/helicase activities are likely required for the activation of other mRNA decay enzymes and the mRNA‐protein complex dissociation to complete NMD. At present, a variety of tools are available that can specifically suppress NMD, and it has become possible to examine the contribution of NMD in a variety of physiological and pathological conditions.
High Proportion of Granzyme B+ Intraepithelial Lymphocytes Contributes to Epithelial Apoptosis in Helicobacter pylori‐Associated Lymphocytic Gastritis
Authors: Han Song‐Hee , Joo Mee , Kim Kyoung‐Mee
Published: January 2013

Background

Helicobacter pylori infection has been linked to the development of lymphocytic gastritis (LG) characterized by ≥25 intraepithelial lymphocytes (IELs) per 100 epithelial cells. We hypothesize that the changes in the subpopulation and/or cytotoxicity of IELs leading to epithelial cell apoptosis may be involved in the pathogenesis of H. pylori‐associated LG.

Materials and Methods

We examined IEL subpopulations and the expression of cytotoxic molecules by IELs in biopsy specimens from 36 patients with H. pylori‐associated LG by immunostainings for CD3, CD4, CD8, T‐cell‐restricted intracellular antigen‐1 (TIA‐1), and granzyme B (GrB) and compared the results with those obtained from 49 patients with H. pylori‐associated gastritis (HPG). To investigate whether the IEL‐mediated cytotoxicity is related to the increase of epithelial apoptosis, we performed a terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay using ApopTag detection kit.

Results

Between LG and HPG groups, significant differences in the number of CD3+, CD4+, CD8+, TIA‐1+ or GrB+ IELs, and ApopTag indices were found. Among the CD3+ IELs, the proportion of CD8+ IELs or TIA‐1+ IELs did not differ between two groups. The LG group showed a selective increase in GrB‐positive, phenotypically activated IELs, which was paralleled by an increase in ApopTag indices. In contrast, the HPG group showed more heterogeneous IEL subpopulations with more CD4+ IELs and less GrB+ IELs compared with the LG group, and we did not find any significant variable contributing to the epithelial apoptosis in the HPG group.

Conclusions

This study shows that in addition to the numerical increase in the IELs, there are significant changes in the subpopulations and cytotoxicity of IELs between HPG and H. pylori‐associated LG. In particular, enhanced GrB‐associated cytotoxicity of the IELs in H. pylori‐associated LG contributes to an increase in epithelial apoptosis.
Advanced hepatocellular carcinoma with lymph node metastases showing epithelial to mesenchymal transition effectively treated with systemic chemotherapy: Report of a case
Authors: Sadamori Hiroshi , Yagi Takahito , Shigeyasu Kunitoshi , Umeda Yuzo , Sugihara Masahiro , Yokomichi Naosuke , Ohara Toshiaki , Nishida Naoshi , Nagasaka Takeshi , Goel Ajay , Fujiwara Toshiyoshi
Published: January 2013

We present a case in which combination chemotherapy was used to successfully treat hepatocellular carcinoma (HCC) with rapid progression of lymph node (LN) metastases after liver resection. In addition, epithelial to mesenchymal transition (EMT) markers were examined immunohistochemically. A 43‐year‐old man who had been diagnosed with HCC showed an enlarged LN near the hepatic artery proper. After extended left lobectomy with lymphadenectomy in the hepatoduodenal ligament, he experienced rapid progression of metastases to the para‐aortic and mediastinal LN. Partial remission was achieved after induction and maintenance of combination chemotherapy using etoposide, carboplatin, epirubicin and 5‐fluorouracil. As a consequence of this treatment, the patient survived 10 months. Immunohistochemical studies demonstrated that HCC cells in the metastatic LN showed low expression of E‐cadherin and high expression of N‐cadherin and vimentin, indicating EMT. Combination chemotherapy may prove effective for patients with HCC accompanied by LN metastases that show features of EMT.
Characterisation of malolactic conversion by Oenococcus oeni to reduce the acidity of apple juice
Authors: Gao Jingfei , Vasantha Rupasinghe H.P. , Pitts Nancy L.
Published: January 2013

The high concentration of malic acid is responsible for the acidity and sourness in apple juice. Bio‐conversion of malic acid to lactic acid through malolactic conversion (MC) in apple juice using Oenococcus oeni was investigated. When apple juice was inoculated with O. oeni (1 × 106 CFU mL−1), over 90% of malic acid was converted into lactic acid within 96 h at room temperature. When pH of apple juice was adjusted to 4.1 prior to inoculation, MC was completed within 60 h. MC was enhanced at a higher temperature (30°C) when compared with room temperature. The rate of MC was directly proportional to the number of bacteria added and MC was completed within 24 h at 1 × 109 CFU mL−1 initial cell density. MC occurred equally under aerobic and anaerobic conditions. The sensory analysis of partial MC‐applied juice when compared against control revealed potential for use of MC for manufacture of low‐acid apple juice.
Antioxidant activity and antimicrobial properties of phenolic extracts from acerola (Malpighia emarginata DC) fruit
Authors: Delva Lemâne , Goodrich‐Schneider Renée
Published: January 2013

The antioxidant activity and antimicrobial property of phenolic extracts from acerola (Malpighia emarginata DC) fruit were assessed. The contribution of ascorbic acid and phenolic compounds in the total antioxidant capacity of the extracts was also evaluated. The extracts showed high total phenolic values and possessed high antioxidant activity as expressed by 2,2′‐diphenylpicrylhydrazyl (DPPH) and oxygen radical absorbance capacity assays (ORAC). The ascorbic acid content ranged from 405 to 1744 mg/100 g of fruit on a fresh weight basis. The antioxidant capacity of the phenolic fractions was in the following order: anthocyanins<phenolic acids<flavonoids. The phenolic fractions contributed 7.1–36.5% of the antioxidant activity expressed by ORAC, whereas the contribution of ascorbic accounted for 18–39% of the total activity. Selected extracts from the flavonoids fraction showed some activity against Staphylococcus aureus.
Comparative study on antioxidant activity of four varieties of Flammulina velutipes with different colour
Authors: Zhang Zuofa , Jin Qunli , Lv Guoying , Fan Lijun , Pan Huijuan , Fan Leifa
Published: January 2013

Flammulina velutipes is one of the most popular edible mushrooms consumed all around the world. This study evaluates the antioxidant potential of four varieties of F. velutipes with different colour (snowy white, off‐white, yellow, snuff colour) in terms of DPPH scavenging activity, reducing power, hydroxyl radical scavenging activity and metal chelating activity. The total phenols, phenolic acid and l‐ergothioneine contents in the four varieties of F. velutipes were also determined. Extracts from yellow F. velutipes demonstrated better antioxidant activities in DPPH, hydroxyl radical and metal chelating activity and extracts from snowy white F. velutipes showed higher activity in reducing power. However, snuff colour F. velutipes exhibited the lowest antioxidant activity in all the tested assays. The antioxidant activities may be attributed to the higher phenolic acid and l‐ergothioneine contents as a linear relation was observed between the two components and the antioxidant parameters.
Evaluation of mungbean protein isolates at various levels as a substrate for microbial transglutaminase and water binding agent in pork myofibrillar protein gels
Authors: Lee Hong C. , Chin Koo B.
Published: January 2013

The objective of this study was to investigate the effect of mungbean protein isolate (MPI) on the potential possibility of water binding agent and as a substrate for the microbial transglutaminase (MTGase) in myofibrillar protein. Cooking loss (CL,%), gel strength (GS, gf), sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE), differential scanning calorimetry (DSC) and scanning electron microscopy (SEM) were measured. The addition of MPI reduced CL, indicating that it has a water binding capacity during cooking. The major protein band (53 kDa) of MPI appeared when MPI was mixed with MP, but it disappeared when MTGase was incorporated. MPI treatment changed the endothermic peaks as compared with those of CTL. MTGase (1%) mediated pork MP increased CL and GS (P < 0.05), and reduced peak temperatures with vanishing of endothermic intensity at 1st and 3rd peaks, suggesting the structural changes of protein gelation. In microstructures, MTGase treatment showed a finely stranded structure in MP gels, while MPI showed a conglomerated surface in MTGase‐mediated MP gels. These results indicated that MPI appears to be a water binding agent during cooking and function as a substrate for MTGase in MP gelation.
Soybean oil‐chitosan emulsion affects internal quality and shelf‐life of eggs stored at 25 and 4 °C
Authors: Wardy Wisdom , Torrico Damir D. , Herrera Corredor José A. , No Hong Kyoon , Zhang Xiumei , Xu Zhimin , Prinyawiwatkul Witoon
Published: January 2013

Effects of soybean oil (SO), chitosan solution (CH) and their emulsions (SO:CH = 60:40, 50:50 and 40:60 ratios) as coatings on internal quality of eggs stored at 25 and 4 °C, respectively, for 7 and 20 weeks, were evaluated. Eggs coated with SO and SO:CH emulsions maintained grade AA and/or A quality up to 7 weeks at 25 °C and 20 weeks at 4 °C, while noncoated eggs changed from AA to B grade after 2 weeks at 25 °C. Compared with noncoated eggs, shelf‐life of eggs stored at 25 °C was extended for 5 weeks by all SO:CH emulsions. Weight loss of eggs coated with SO:CH emulsions was <3% after 7 weeks at 25 °C and <5% after 20 weeks at 4 °C. SO:CH emulsion is alternatively an effective coating with possible shorter drying times for reducing weight loss and preserving the internal quality of eggs.
Factors influencing intracytoplasmic sperm injection (ICSI) outcome in men with azoospermia
Authors: Abdel Raheem Amr , Rushwan Nagla , Garaffa Giulio , Zacharakis Evangelos , Doshi Alpesh , Heath Carleen , Serhal Paul , Harper Joyce C. , Christopher Nim A. , Ralph David
Published: January 2013

What's known on the subject? and What does the study add?

The management of patients with non‐obstructive azoospermia (NOA) and some cases of obstructive azoospermia involves testicular sperm extraction (TESE or micro‐dissection TESE) combined with intracytoplasmic sperm injection (ICSI). Several studies have investigated the effect of the male age, the cause of azoospermia, testicular histopathology, the type of sperm used, and the use of pentoxyphilline, on the ICSI cycle outcome in men with azoospermia.

The present study showed that none of these factors influenced the ICSI outcome in men with azoospermia, thus once sperm is found in an azoospermic male, no other male factor seems to influence the ICSI outcome. To our knowledge this is the first study to comment on the outcome of ICSI in men with NOA based on testicular histopathology.

Objectives

To access the effect of: male age, the cause of azoospermia (obstructive azoospermia vs non‐obstructive azoospermia [NOA]), testicular histopathology, the type of sperm used (fresh vs frozen‐thawed), and the use of pentoxyphilline on the intracytoplasmic sperm injection (ICSI) cycle outcome in men with azoospermia.

To our knowledge this is the first study to comment on the outcome of ICSI in men with NOA based on testicular histopathology.

Patients and Methods

A retrospective analysis of 137 testicular sperm extraction‐ICSI cycles performed between 2001–2010, involving 103 men with azoospermia, with 26 couples having repeat cycles.

Results

Analysis of the results did not show any statistically significant differences in the fertilization, embryo cleavage, clinical pregnancy, live birth and miscarriage rates in relation to the male age, cuase of azoospermia, testicular histopathology, type of sperm used and the use of pentoxyphilline.

Conclusion

Once sperm is found in a man with azoospermia, no other male factor seems to influence the ICSI outcome.
Congenital completely buried penis in boys: anatomical basis and surgical technique
Authors: Liu Xing , He Da‐wei , Hua Yi , Zhang De‐ying , Wei Guang‐hui
Published: January 2013

What's known on the subject? and What does the study add?

Surgical correction of the congenital completely buried penis (CCBP) is a difficult challenge and there is no unanimous consensus about the surgical ‘gold standard’ and patient eligibility for surgery.

In the present study, dysgenetic fundiform ligaments were found to be attached to the distal or middle shaft of the penis. This abnormality can be successfully corrected by releasing the fundiform ligament and mobilising the scrotal skin to cover the length of the penile shaft. The study shows that the paucity and traction of the penile skin and an abnormal fundiform ligament are important anatomical defects in CCBP. Dorsal curve and severe shortage of penile skin in erectile conditions are the main indications for surgical correction.

Objective

To present our experience of anatomical findings for congenital completely buried penis (CCBP), which has no unanimous consensus regarding the ‘gold standard’ for surgical correction and patient eligibility, by providing our surgical technique and illustrations.

Patients and Methods

Between February 2006 and February 2011, 22 children with a median (range) age of 4.2 (2.5–5.8) years, with CCBP underwent surgical correction by one surgeon.

Toilet training and photographs of morning erections by parents were advised before surgery.

The abnormal anatomical structure of buried penis during the operation was observed. The technique consisted of the release of the fundiform ligament, fixation of the subcutaneous penile skin at the base of the degloved penis, penoscrotal Z‐plasty and mobilisation of the penile and scrotal skin to cover the penile shaft.

Results

In reflex erectile conditions, CCBP presents varying degrees of dorsal curve and shortage of penile skin.

Dysgenetic fundiform ligaments were found to be attached to the distal or middle shaft of the penis in all patients.

All wounds healed well and the cosmetic outcome was good at 6‐month follow‐up after the repair.

Conclusion

The appearance of the dorsal curve in CCBP mainly results from the traction of penile dorsal skin and the abnormal attachment of the fundiform ligament to the shaft. This abnormality can be successfully corrected by releasing the abnormal fundiform ligament and mobilising scrotal skin to cover the length of the penile shaft.
Extracorporeal shockwave lithotripsy to distal ureteric stones: the transgluteal approach significantly increases stone‐free rates
Authors: Phipps Simon , Stephenson Carolann , Tolley David
Published: January 2013

What's known on the subject? and What does the study add?

Shockwave lithotripsy (SWL) can be used to treat stones at any position within the ureter, as long as the stone is radio‐opaque and there is a path for the shockwave to reach the stone. However the results of SWL to distal ureteric calculi, with the patient in a prone position, were inferior to those of treating stones within the upper ureter.

The transguteal approach allows the lithotripsy shockwave to reach the lower ureter via the greater selatle foramen. This study shows that this approach for SWL to distal ureteric calculi is more effective than the prone approach.

Objective

To compare the outcomes of extracorporeal shockwave lithotripsy (ESWL) for distal ureteric stones treated using the prone and transgluteal (supine) approaches in a tertiary referral stone unit using a fourth generation lithotriptor.

Patients and Methods

We selected consecutive patients undergoing ESWL to distal ureteric stones over 1 year, during which we changed our treatment protocol from a prone to transgluteal (supine) approach.

Patients were treated using the Sonolith Vision Lithotriptor (Technomed Medical Systems, Vaulx‐en‐Velin, France).

Outcome was assessed using plain abdominal film of kidney, ureter and bladder (KUB) X‐ray taken at 2 weeks then monthly as required.

Treatment success was defined as complete clearance of stone fragments and treatment failure was defined as persistence of stone fragments beyond 3 months or the need for ureteroscopy.

Results

A total of 38 patients were treated in the prone position and 72 patients using a transgluteal approach.

Patient and stone characteristics were identical in both groups. The mean (range) stone size was 7.8 (4–16) mm.

The proportions of patients who were stone‐free after one treatment session within the prone and transgluteal treatment groups were 40 and 78%, respectively (<0.001).

The overall success rates for treatment within the prone and transgluteal groups were 63 and 92%, respectively (<0.001).

Conclusions

Transgluteal ESWL to stones within the distal ureter leads to significantly higher stone‐free rates than treatment using the prone approach.

The majority of patients are rendered stone‐free after one session of treatment and the overall success rates are similar to those of ureteroscopic management.
Comparison of musculoskeletal anatomic relationships, determined by magnetic resonance imaging, in postpubertal female patients with and without classic bladder exstrophy
Authors: Anusionwu Ifeanyi , Tekes Aylin , Stec Andrew A. , Gearhart John P. , Wright E. James
Published: January 2013

What's known on the subject? and What does the study add?

Several studies in the paediatric literature have characterized the pelvic musculoskeletal anatomy of infants and children with bladder exstrophy using MRI and three‐dimensional CT. The pelvic floor anatomy of female patients with bladder exstrophy who have undergone somatic growth and puberty is less well described.

This study uses MRI to characterize comprehensively the pelvic anatomy of postpubertal females with classic bladder exstrophy by measuring 15 pelvic floor variables previously described in younger children with bladder exstrophy.

Objective

To characterize pelvic musculoskeletal anatomy in postpubertal females with classic bladder exstrophy, and to compare this with females without bladder exstrophy.

Patients and Methods

The authors reviewed the medical records of all females in our institutional review board‐approved bladder exstrophy database of 1078 patients and identified those with classic bladder exstrophy who underwent pelvic magnetic resonance imaging (MRI) after the age of 12 years.

Indications for MRI included haematuria, adnexal lesion, perineal fistula, non‐pelvic cancer staging, abdominal wall hernia and vaginal stenosis.

Age‐ and race‐matched female patients without exstrophy who underwent MRI evaluation for similar indications were included for comparison.

The MRI protocol included axial, sagittal and coronal T1‐ and/or T2‐weighted imaging.

Results

The study included 30 patients with a median (range) age of 22.5 (12–55) years at time of MRI. Ten patients had bladder exstrophy while 20 control patients did not.

A smaller percentage of levator ani was located in the anterior compartment of the pelvis in patients with bladder exstrophy compared with controls.

The iliac wing angle, puborectalis angle, ileococcygeous angle, levator ani width, symphyseal diastasis, erectile body diastasis, posterior bladder neck distance and posterior anal distance was greater in patients with bladder exstrophy than in those without.

The ischial angle and obturator internus angle were narrower in patients with bladder exstrophy than in those without, and there was no significant difference between levator ani surface area, sacral anal angle, sacral bladder neck angle and bladder neck erectile body distance between the two patient groups.

Conclusions

In postpubertal females with bladder exstrophy, significant deviations from normal pelvimetry exist, including posterior location of the majority of the levator ani muscle, a wider ileococcygeous angle and a wider symphyseal diastasis.

These differences are similar to those described in previous comparisons of younger children with bladder exstrophy and control children.
Serum receptor activator of nuclear factor κB ligand (RANKL) levels predict biochemical recurrence in patients undergoing radical prostatectomy
Authors: Todenhöfer Tilman , Hennenlotter Jörg , Leidenberger Philipp , Wald Alexander , Hohneder Andrea , Kühs Ursula , Mischinger Johannes , Aufderklamm Stefan , Gakis Georgios , Blumenstock Gunnar , Stenzl Arnulf , Schwentner Christian
Published: January 2013

What's known on the subject? and What does the study add?

There is increasing evidence that the receptor activator of nuclear factor κB ligand (RANKL) pathway not only contributes to the development of bone metastases, but also influences tumour biology in earlier stages of cancer.

The study shows that preoperative serum levels of RANKL and its inhibitor osteoprotegerin (OPG) have a prognostic impact in patients undergoing radical prostatectomy for clinically localized prostate cancer. Both high levels of RANKL and a higher RANKL/OPG ratio are independent predictors of early biochemical recurrence in these patients.

Objective

To assess the prognostic impact of proteins of the receptor activator of nuclear factor κB (RANKL) pathway in serum samples from patients undergoing radical prostatectomy.

Patients and Methods

We retrospectively determined soluble RANKL (sRANKL) and osteoprotegerin (OPG) by ELISA in serum samples of 178 patients undergoing radical prostatectomy between 2004 and 2006.

Clinical and patient follow‐up data were analysed using the Wilcoxon–Mann–Whitney test, the Kaplan–Maier method, and single variable or multifactorial Cox proportional hazards analysis.

Results

Higher serum sRANKL levels (P = 0.01), lower serum OPG levels (P = 0.01) and a higher sRANKL/OPG ratio (P = 0.004) were significant risk factors for biochemical recurrence (BCR).

In multifactorial analysis, adjusted for the common risk factors for BCR, sRANKL and sRANKL/OPG ratio were confirmed as independent prognostic factors.

Neither sRANKL nor OPG showed a clear association with histopathological factors such as pT stage, pN Gleason score or resection margin status, nor were they associated with prostate‐specific antigen level.

Conclusions

Greater activity of the RANKL pathway in the serum of patients with prostate cancer undergoing radical prostatectomy is a risk factor for BCR.

The RANKL pathway seems to contribute to the biological behaviour of prostate cancer even at the organ‐confined stage of the disease.
Bladder preservation in the treatment of muscle‐invasive bladder cancer (MIBC): a review of the literature and a practical approach to therapy
Authors: Smith Zachary L. , Christodouleas John P. , Keefe Stephen M. , Malkowicz S. Bruce , Guzzo Thomas J.
Published: January 2013

What's known on the subject? and What does the study add?

Bladder preservation therapies for muscle‐invasive bladder cancer (MIBC) have been developed to address the needs of two cohorts: patients with severe medical co‐morbidities for whom radical cystectomy is too high risk and patients with limited disease who wish to avoid aggressive surgery. There are multiple bladder preservation options, although the trimodal approach of maximal transurethral resection with chemoradiotherapy is the most strongly supported. While outcomes are worse for patients unfit for surgery than those otherwise fit for surgery, bladder preservation approaches still offer curative potential.

We present a comprehensive review of the literature and outline a practical approach to bladder preservation therapy for MIBC. This review aims to help urologists easily navigate through the decision tree of therapeutic options.

Radical cystectomy (RC) is associated with considerable morbidity. Aside from the perioperative period, RC with urinary diversion poses great potential for long‐term complications and morbidity.

Bladder preservation therapies for muscle‐invasive bladder cancer (MIBC) have been developed to address the needs of two cohorts: patients with severe medical co‐morbidities for whom a radical surgery is too high risk and patients with limited disease who wish to avoid radical surgery.

The goal of achieving complete response to treatment while maintaining bladder form and function has led to the development of multimodal approaches to this disease.

There are multiple bladder preservation options, although the trimodal approach of maximal transurethral resection with chemoradiotherapy is the most strongly supported.

In medically operable patients (‘fit’ for surgery), there is abundant evidence to support trimodal therapy as an acceptable treatment option for highly selected patients with MIBC with favourable pathological parameters.

While outcomes are worse for medically inoperable patients (‘unfit’ for surgery), bladder preservation approaches still offer curative potential. However, prospective trials comparing the above regimens to RC are still needed to better define their role in the treatment of MIBC.

We present a comprehensive review of the literature and outline a practical approach to bladder preservation therapy for MIBC.
Measurement of greenhouse gas emissions from agriculture: economic implications for policy and agricultural producers*
Authors: Thamo Tas , Kingwell Ross S. , Pannell David J.
Published: January 2013

If agriculture were to be included in Australia’s carbon price scheme, a key decision for government would be how to estimate greenhouse gas emissions. We explore the consequences of three different methods for measuring on‐farm emissions: national accounting methods, an amended version of those methods and use of best‐available local data. Estimated emissions under the three methods can vary widely; for example, on a case study farm in Western Australia, local data indicated 44 per cent lower emissions than did the national accounts method. If on‐farm emissions are subject to an emissions price, the impact on farm profit is large and varies considerably with different measurement methods. For instance, if a price of $23/t of CO2‐e applies then farm profit falls by 14.4–30.8 per cent depending on the measurement method. Thus, the choice of measurement method can have large distributional consequences. On the other hand, inaccurate measurement results in relatively minor deadweight losses. On‐farm sequestration through reafforestation may lessen the impact of an emissions price on farm businesses, although it will require a high carbon price to be viable, especially if sequestration rates are underestimated or low.
Quantifying Phosphorus Flow Pathways Through Socioeconomic Systems at the County Level in China
Authors: Bi Jun , Chen Qinqin , Zhang Ling , Yuan Zengwei
Published: January 2013

Phosphorus (P) is a key factor in aquatic eutrophication, and P contamination has become a common issue worldwide. Many developing countries, including China, have made great efforts in the anti‐P contamination battle. In this article we mainly discuss the P flow in Wuwei, a typical county in China with insufficient wastewater treatment, using the method of static substance flow analysis. We show that characterizing P metabolic pathways and flows at the county level can provide useful information about P pollution. Through complex calculations, we found that Wuwei County released 3,552 metric tons (t) of P into the local aquatic environment in 2008 and that its P load (3.35 kilograms P per capita per year [kg P/cap/yr] or 19.43 kilograms P per hectare per year [kg‐P/ha/yr]) was greater than both the adjoining counties’ and Chaohu City's average levels combined. The agricultural subsystem discharged the largest quantity of P (2,572 t) and had a relatively low production conversion efficiency (32%) and P waste recycling rate (36%). The rural residential and small‐scale livestock breeding systems also accounted for substantial portions of P discharge. Anti‐P contamination efforts should consequently focus on those three subsystems. Based on the results of this case study, we also discuss the feasibility of potential efforts to reduce P contamination.
Impedance Spectroscopy Characterization in Bipolar Ta/MnOx/Pt Resistive Switching Thin Films
Authors: Park Chan‐Rok , Choi Sun‐Young , You Yil‐Hwan , Yang Min Kyu , Bae Seung‐Muk , Lee Jeon‐Kook , Hwang Jin‐Ha
Published: January 2013

Impedance spectroscopy was applied to MnOx‐based thin films prepared in symmetric and asymmetric electrode configurations, i.e., Pt/MnOx/Pt and Ta/MnOx/Pt, respectively. Equivalent circuit analysis suggests the presence of higher resistance surface layers adjacent the electrodes, in addition to a higher conductivity component at central portions of the MnOx thin films. The asymmetric configuration enables the Ta/MnOx interfacial layer to facilitate the redox transport of oxygen ions, where significant changes in resistance with the electric field are responsible for the higher on/off resistance ratio in Ta/MnOx/Pt. The higher dielectric constant and bias‐dependent capacitance and resistance support the coexistence of both oxidized surfaces and interfacial layers.
RAMESES publication standards: meta‐narrative reviews
Authors: Wong Geoff , Greenhalgh Trish , Westhorp Gill , Buckingham Jeanette , Pawson Ray
Published: January 2013

Background

Meta‐narrative review is one of an emerging menu of new approaches to qualitative and mixed‐method systematic review. A meta‐narrative review seeks to illuminate a heterogeneous topic area by highlighting the contrasting and complementary ways researchers have studied the same or a similar topic. No previous publication standards exist for the reporting of meta‐narrative reviews. This publication standard was developed as part of the RAMESES (Realist And MEta‐narrative Evidence Syntheses: Evolving Standards) project. The project's aim is to produce preliminary publication standards for meta‐narrative reviews.

Design

A mixed method study synthesising data between 2011 to 2012 from a literature review, online Delphi panel and feedback from training, workshops and email list.

Methods

We: (a) collated and summarized existing literature on the principles of good practice in meta‐narrative reviews; (b) considered the extent to which these principles had been followed by published reviews, thereby identifying how rigor may be lost and how existing methods could be improved; (c) used a three‐round online Delphi method with an interdisciplinary panel of national and international experts in evidence synthesis, meta‐narrative reviews, policy, and/or publishing to produce and iteratively refine a draft set of methodological steps, and publication standards; (d) provided real‐time support to ongoing meta‐narrative reviews and the open‐access RAMESES online discussion list so as to capture problems and questions as they arose; and (e) synthesized expert input, evidence review, and real‐time problem analysis into a definitive set of standards.

Results

We identified nine published meta‐narrative reviews, provided real‐time support to four ongoing reviews, and captured questions raised in the RAMESES discussion list. Through analysis and discussion within the project team, we summarized the published literature, and common questions and challenges into briefing materials for the Delphi panel, comprising 33 members. Within three rounds this panel had reached consensus on 20 key publication standards, with an overall response rate of 90%.

Conclusions

This project used multiple sources to draw together evidence and expertise in meta‐narrative reviews. For each item we have included an explanation for why it is important and guidance on how it might be reported. Meta‐narrative review is a relatively new method for evidence synthesis and as experience and methodological developments occur, we anticipate that these standards will evolve to reflect further theoretical and methodological developments. We hope that these standards will act as a resource that will contribute to improving the reporting of meta‐narrative reviews.