bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study
Authors: Landa M. , Cottrell M. T. , Kirchman D. L. , Kaiser K. , Medeiros P. M. , Tremblay L. , Batailler N. , Caparros J. , Catala P. , Escoubeyrou K. , Oriol L. , Blain S. , Obernosterer I.
Published: August 2013

Dissolved organic matter (DOM) and heterotrophic bacteria are highly diverse components of the ocean system, and their interactions are key in regulating the biogeochemical cycles of major elements. How chemical and phylogenetic diversity are linked remains largely unexplored to date. To investigate interactions between bacterial diversity and DOM, we followed the response of natural bacterial communities to two sources of phytoplankton‐derived DOM over six bacterial generation times in continuous cultures. Analyses of total hydrolysable neutral sugars and amino acids, and ultrahigh resolution mass spectrometry revealed large differences in the chemical composition of the two DOM sources. According to 454 pyrosequences of 16S ribosomal ribonucleic acid genes, diatom‐derived DOM sustained higher levels of bacterial richness, evenness and phylogenetic diversity than cyanobacteria‐derived DOM. These distinct community structures were, however, not associated with specific taxa. Grazing pressure affected bacterial community composition without changing the overall pattern of bacterial diversity levels set by DOM. Our results demonstrate that resource composition can shape several facets of bacterial diversity without influencing the phylogenetic composition of bacterial communities, suggesting functional redundancy at different taxonomic levels for the degradation of phytoplankton‐derived DOM.
Phenotypic heterogeneity is a selected trait in natural yeast populations subject to environmental stress
Authors: Holland Sara L. , Reader Tom , Dyer Paul S. , Avery Simon V.
Published: August 2013

Populations of genetically uniform microorganisms exhibit phenotypic heterogeneity, where individual cells have varying phenotypes. Such phenotypes include fitness‐determining traits. Phenotypic heterogeneity has been linked to increased population‐level fitness in laboratory studies, but its adaptive significance for wild microorganisms in the natural environment is unknown. Here, we addressed this by testing heterogeneity in yeast isolates from diverse environmental sites, each polluted with a different principal contaminant, as well as from corresponding control locations. We found that cell‐to‐cell heterogeneity (in resistance to the appropriate principal pollutant) was prevalent in the wild yeast isolates. Moreover, isolates with the highest heterogeneity were consistently observed in the polluted environments, indicating that heterogeneity is positively related to survival in adverse conditions in the wild. This relationship with survival was stronger than for the property of mean resistance (IC50) of an isolate. Therefore, heterogeneity could be the major determinant of microbial survival in adverse conditions. Indeed, growth assays indicated that isolates with high heterogeneities had a significant competitive advantage during stress. Analysis of yeasts after cultivation for ≥ 500 generations additionally showed that high heterogeneity evolved as a heritable trait during stress. The results showed that environmental stress selects for wild microorganisms with high levels of phenotypic heterogeneity.
Renal Replacement Therapy in Slovenia: Excerpts From 2011 Data
Authors: Buturović‐Ponikvar Jadranka , Gubenšek Jakob , Arnol Miha , Adamlje Tone , Blanuša Danica , Ceglar Zlata , Steklasa Sonja Cimerman , Černe Senka , Čufer Andrej , Drozg Andrej , Ekart Robert , Guček Andrej , Kandus Aljoša , Kapun Sonja , Kralj‐Lopert Simona , Klančič Dimitrij , Kunc‐Rešek Natalija , Kralj Stojan , Malovrh Marko , Močivnik Marjan , Novljan Gregor , Ponikvar Rafael , Rus Igor , Saksida Silvan , Vujkovac Bojan
Published: August 2013

This report provides a summary of the 2011 Slovenian renal replacement therapy (RRT) data. Data were obtained from 24 renal centers: 23 dialysis and one transplant center, referred as of 31 December 2011, with 100% response rate to individual patient questionnaires. Slovenia has a population of approximately 2 million (2 052 496 in 2011). The total number of patients treated by RRT was 2011,that is, 980 per million of population (pmp); 0.4% decrease compared to 2010. 1347 (67.0%) were treated by hemodialysis, 60 (3.0%) by peritoneal dialysis, and 604 (30.0%) had a functioning kidney graft. A total of 236 incident patients, 115 pmp (at day one), started RRT, their median age was 68 years, 64.8% were men, 36.4% were diabetics. Regarding hemodialysis patients, 59.3% were treated with on‐line hemodiafiltration, 86% with ultrapure dialysis fluid. Median weekly duration of hemodialysis was 12.5 h, median dry body weight 70 kg, mean blood flow 275 ± 46 mL/min, 7.1% were dialyzed in a single‐needle mode. Vascular accesses were native arteriovenous fistula in 79%, polytetrafluoroethylene graft in 6%, and catheter in 15%. The crude death rate was 15.9% in dialysis patients, 1.9% in transplant recipients, and 12.0% in all RRT patients (both dialysis and transplant, incident patients at day 1 included). Slovenia has been a member of Eurotransplant since 2000. Forty‐six kidney transplantations were performed in 2011, all from deceased donors. A slight decrease in prevalent number of RRT patients was observed in 2011, for the first time in 40 years. The number and proportion of patients with functioning kidney grafts is increasing, reaching 30% in 2011.
Chronic Kidney Disease Progression to End Stage Renal Disease: A Single Center Experience of the Role of the Underlying Kidney Disease
Authors: Ekart Robert , Ferjuc Anita , Furman Barbara , Gerjevič Špela , Bevc Sebastjan , Hojs Radovan
Published: August 2013

Chronic kidney disease (CKD) is common and several factors affect its progression to end‐stage renal disease (ESRD). The main goal of our study was to assess the influence of underlying kidney disease and some other important factors during the time of CKD progression to ESRD. A retrospective study of 91 patients (57 men, 34 women; average age 57.7 ± 13.2 years) was carried out. Patients were monitored at least one month before the first renal replacement treatment (RRT). Estimated glomerular filtration rate (eGFR) at first referral to nephrologist was determined by Modification of Diet in Renal Disease equation. Proteinuria was assessed semiquantitatively with dipsticks. Thirty‐five patients (38.5%) had diabetic nephropathy (DN), 21 (23.1%) hypertensive nephrosclerosis (HN), 21 (23.1%) adult polycystic kidney disease (APKD) and 14 (15.4%) immunoglobulin A nephropathy (IgAN). Average eGFR at first referral for DN patients was 20.1, and then 23.4 for HN, 35.5 for APKD, and 36.4 mL/min per 1,73 m2 for IgAN patients. Average time between first nephrological visit and first RRT was 28.4 months for DN patients, 41 for HN, 80.8 for APKD, and 70.1 for IgAN patients. Comparison of all four groups of CKD patients showed that in patients with APKD and IgAN impairment of kidney function to ESRD had progressed statistically significantly slower (P < 0.001). When eGFR at referral, proteinuria, smoking, and renin‐angiontensin‐aldosterone blockade treatment had been added into the model, patients with APKD and IgAN had a statistically significant longer period between first nephrological visit and first RRT (P < 0.026). In comparison with patients with other underlying causes of CKD, patients with APKD and IgAN had a statistically significant slower progression rate of CKD to ESRD.
Effect of Switching to Nocturnal Thrice‐Weekly Hemodialysis on Clinical and Laboratory Parameters: Our Experience
Authors: Gubenšek Jakob , Buturović‐Ponikvar Jadranka , Knap Bojan , Marn Pernat Andreja , Benedik Miha , Ponikvar Rafael
Published: August 2013

Long or frequent hemodialysis schedules are reported to improve clinical outcomes. We report here our experience with an in‐center, nocturnal, thrice‐weekly hemodialysis program. We retrospectively analyzed the effect of switching 10 patients (8 male, age 45 ± 11 years, renal replacement therapy vintage 12 ± 8 years) from regular, 4–5 h, thrice‐weekly hemodialysis to 8 h nocturnal, in‐center hemodialysis as regards dialysis efficiency, chronic kidney disease‐metabolic and bone disease (CKD‐MBD) parameters, blood pressure, and anemia. With more intense dialysis, the mean predialysis creatinine and urea decreased significantly (1092 ± 195 vs. 961 ± 154 μmol/L, P < 0.01 and 30.8 ± 4.6 vs. 25.5 ± 2.9 mmol/L, P < 0.01), while the decrease in potassium was insignificant (5.9 ± 0.7 vs. 5.6 ± 0.5 mmol/L), but in 3/10 patients, dialysate potassium was increased. Three months after starting nocturnal hemodialysis, no significant influence on pre‐dialysis blood pressure was observed (143/80 vs. 140/80 mmHg), but antihypertensive medications were reduced in two patients. The mean dry weight reduced (74 ± 12 to 72 ± 12 kg) and the mean ultrafiltration increased insignificantly (3123 ± 1174 to 3434 ± 1341 mL). Serum calcium was stable, while phosphate reduced insignificantly (1.5 ± 0.5 to 1.2 ± 0.2 mmol/L), but 6/10 patients were able to discontinue phosphate binders, the dose was reduced in one, and phosphate was added to dialysate in 3/10 patients. Intact parathyroid hormone values were within the target range, except in patients post‐parathyroidectomy. There were no differences in hemoglobin (121 ± 6 vs. 122 ± 8 g/L), and the mean epoetin dose decreased insignificantly (5950 ± 3947 vs. 5250 ± 4238 IU/week). To conclude, improved phosphate and potassium control and reduction in phosphate binders were observed after switching to nocturnal hemodialysis. There was an insignificant reduction of epoetin dose and antihypertensive medications.
Arteriovenous Grafts in the Thigh: An Excellent Hemodialysis Vascular Access When Arm Vasculature Is Exhausted
Authors: Ponikvar Rafael
Published: August 2013

The aim of our retrospective analysis with prospective collected data was to evaluate the patency of thigh expanded polytetrafluoroethylene (ePTFE) arteriovenous (AV) grafts, which were placed in chronic hemodialysis patients by the same interventional nephrologist skilled in hemodialysis access vascular surgery. From February 1991 until March 2013, 35 thigh ePTFE grafts were placed in 31 chronic hemodialysis patients. Twenty (57%) were women, mean age 58.7 ± 14.5, dialysis vintage 11.9 ± 7.3 years, mean number of previous vascular accesses 4.4 ± 1.9. Two of the 35 (5.7%) grafts were lost to follow‐up, immediate failure occurred in 1/35 (2.8%) grafts, and thrombosis appeared within 30 days in 2/35 (5.7%) grafts. Four of the 31 patients died with functioning grafts, while in 9/31 patients the grafts are still patent. In the remaining 17 AV grafts that thrombosed, no surgical intervention was performed in 8/17, while 18 thrombectomies (two per graft) were performed in 9/17 to maintain graft patency. The immediate success rate was 97.1%. Primary patency was from 0–3251 days, on average 906 ± 898, median 472, cumulative patency (N = 33) was from 0–3251 days, on average 1174 ± 954, median 966. Cumulative patency of the grafts that were patent for more than 30 days (N = 30) was from 153–3251 days, on average 1298 ± 921, median 1207. The ePTFE graft survival after the 1st year was 78%, after the 2nd year 74%, after the 3rd year 66%, after the 4th year 56%, after the 5th year 52%, and after the 9th year 13 %. The longest patency was 3251 days without any intervention. Steal syndrome occurred in two patients after 2522 and 275 days after fistula placement.
Influence of Renin‐Angiotensin‐Aldosterone System‐Blocking Drugs on Peritoneal Membrane in Peritoneal Dialysis Patients
Authors: Trošt Rupnik Alijana , Pajek Jernej , Guček Andrej , Osredkar Joško , Kovač Damjan , Bren Andrej , Klančič Dimitrij , Saksida Silvan , Rus Igor , Globokar Mateja , Drozg Andrej , Lešnik Marjeta , Plešivčnik Zala , Ekart Robert , Lopert Simona , Lindič Jelka
Published: August 2013

Therapy with renin‐angiotensin‐aldosterone system (RAAS)‐blocking drugs prevents the development of fibrosis and angiogenesis in animal models and humans. In our study we have evaluated the systemic effect of RAAS blockade and the effect on peritoneal growth factors, cytokine production and membrane transport characteristics in patients on peritoneal dialysis. Thirty‐seven peritoneal dialysis (PD) patients were enrolled in our cross‐sectional study. Aldosterone and angiotensin II concentrations were measured in serum to determine the RAAS activity. The inflammatory and profibrotic activity was evaluated by measuring the concentration of C‐reactive protein (CRP), serum albumin, and peritoneal concentration of interleukin‐6 (IL‐6), vascular endothelial growth factor (VEGF), plasminogen activator inhibitor‐1 (PAI‐1), transforming growth factor‐β (TGF‐β) and cancer antigen‐125 (CA‐125). The transport characteristics of the peritoneal membrane were analyzed with a peritoneal equilibration test (PET). Results were compared between the group with RAAS‐blocking drugs (RAAS group) and the group without them (non‐RAAS group). Mean serum aldosterone concentration was significantly lower in patients treated with ARB‐blocking drugs (P = 0.001) and serum angiotensin II concentration was lower in patients treated with ACE inhibitors (P = 0.009). RAAS blockade resulted in lower peritoneal PAI‐1 levels (748.1 to 1222.7 ng/L; P = 0.07) without any influence on CRP, peritoneal concentrations of IL‐6, VEGF, TGF‐β and CA‐125, or alteration in peritoneal membrane characteristics tested by PET. RAAS‐blocking drugs could be effective in preventing peritoneal fibrosis due to possible reduction of peritoneal PAI‐1 concentrations that have already been etiologically linked with fibrin deposition in the pathogenesis of encapsulating peritoneal sclerosis.
Capturing the population structure of microparasites: using ITS‐sequence data and a pooled DNA approach
Authors: Giessler Sabine , Wolinska Justyna
Published: August 2013

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a common marker not only for the molecular identification of different taxa and strains, but also for the analysis of population structure of wild microparasite communities. Importantly, the multicopy nature of this region allows the amplification of low‐quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS‐types [as identified by statistical parsimony network analysis (SPN)] is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency in detecting different sequence types was even higher after sample pooling. As shown by simulations, an easily manageable number of sequences from pooled DNA samples are sufficient to resolve the spatial population structure in this system. In summary, the ITS region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, the application of SPN analysis is a good alternative to the well‐established neighbour‐joining method (NJ) for the identification of representative ITS‐types. SPN can even outperform NJ by joining most of the singleton sequences to representative sequence clusters.
Restructuring of the amphibian gut microbiota through metamorphosis
Authors: Kohl Kevin D. , Cary Tawnya L. , Karasov William H. , Dearing M. Denise
Published: August 2013

Vertebrates maintain complex symbioses with a diverse community of microbes residing within their guts. The microbial players in these symbioses differ between major taxa of vertebrates, such that fish and amniotes maintain notably different communities. To date, there has not been a culture‐independent inventory of an amphibian gut microbial community. Here, we compared gut microbial communities of tadpoles and frogs of the Northern leopard frog (Lithobates pipiens). We utilized Illumina sequencing, which allowed us to inventory more than 450 000 microbial sequences. We found that tadpoles and frogs differ markedly in the composition of their gut microbial communities, with tadpoles maintaining a community more similar to fish, whereas the frog community resembles that of amniotes. Additionally, frogs maintain a community with lower phylogenetic diversity compared with tadpoles. The significant restructuring of the microbiota is likely due to changes in diet as well as the large reorganization of the intestinal organ during metamorphosis. Overall, we propose that amphibians represent an important system in which to study regulation and selection of gut microbial communities.
Regional Specialisation of the Ganglion Cell Density in the Retina of the Native Duck (Anas platyrhynchos) of Bangladesh
Authors: Uddin M. , Quasem M. A. , Rhaman M. L.
Published: August 2013

In this study, retinal whole‐mount specimens were prepared and stained with 0.1% cresyl violet for the ganglion cell study in the native duck (Anas platyrhynchos). The total number, distribution and size of these cells were determined in different retinal regions. The mean total number of ganglion cells was 1 598 501. The retinal area centralis had the highest ganglion cell density with 11 200 cells/mm2. Number of ganglion cell bodies was the highest in temporal area, followed by dorsal, nasal and ventral areas. Ganglion cell size ranged from 5.25 to 80 μm2. In the temporal and nasal region, most of the cells were ranged from 15 to 25 μm2, and in the dorsal and ventral region, most of the cells were ranged from 12 to 25 μm2. There was a marked trend for the retinal ganglion cell size to increase as the population density decrease towards the periphery. A population of small ganglion cells persisted into the central area just above the optic disc and the largest soma area was in the ventral zone of the retina. Thus, the specialisation of ganglion cell densities and their sizes support the notion that the conduction of visual information towards the brain from all regions of the retina is not uniform, and the central area is the fine quality area for vision in native duck.
Clinical use of new oral anticoagulant drugs: dabigatran and rivaroxaban
Authors: Baglin Trevor
Published: August 2013

Orally active small molecules that selectively and specifically inhibit coagulation serine proteases have been developed for clinical use. For some patients these oral direct inhibitors (ODIs) offer substantial benefits over oral vitamin K antagonists (VKA). However, for the majority of patients with good anticoagulant control with VKAs the advantages of the ODIs are primarily convenience and few drug interactions. The drugs are prescribed at fixed dose without the need for monitoring or dose adjustment in the majority of patients and the rapid onset of anticoagulation and short half‐life make initiation and interruption of anticoagulation considerably easier than with VKAs. As yet, specific antidotes to ODIs are not available for clinical use but these are in development as rapid reversal agents. As with all anticoagulants produced so far, there is a correlation between intensity of anticoagulation and bleeding. Consequently, the need to consider the balance of benefit and risk in each individual patient is no less important than with VKA therapy. Dabigatran and rivaroxaban have been chosen for this review as examples of a thrombin inhibitor and an inhibitor of factor Xa respectively. The clinical application of these drugs is the focus of the review.
Clofarabine in combination with pegylated asparaginase in the frontline treatment of childhood acute lymphoblastic leukaemia: a feasibility report from the CoALL 08‐09 trial
Authors: Escherich Gabriele , zur Stadt Udo , Zimmermann Martin , Horstmann Martin A. ,   CoALL study group
Published: August 2013

Clofarabine was the latest new drug to be approved, in 2004, for relapsed or refractory acute lymphoblastic leukaemia (ALL). To investigate its value in the frontline treatment of ALL we applied clofarabine 5 × 40 mg/m2 in combination with pegylated asparaginase (PEG‐ASP) 1 × 2500 iu/m2 in high risk ALL patients as a novel post‐induction element in the German Co‐operative Study Group for treatment of ALL (CoALL) trial 08‐09. Newly diagnosed ALL patients, defined by a significant minimal residual disease (MRD) load at the end of induction (B‐progenitor ALL at day 29 ≥ 10−4 and T‐ALL at day 43 ≥ 10−3) were eligible for this phase II trial. All other patients received the standard treatment consisting of high‐dose cytarabine (HIDAC) 4 × 3 g/m² in combination with Peg‐ASP 2500 iu/m². Forty‐two patients (39 B‐progenitor; 3 T‐ALL) fulfilled the criteria, were stratified and received the clofarabine/PEG‐ASP treatment resulting in 24/39 (61%) MRD‐negative B‐progenitor patients compared to 18/39 (46%) after HIDAC/PEG‐ASP in CoALL 07‐03. Overall, the toxicity profile of clofarabine/PEG‐ASP was similar to HIDAC/PEG‐ASP without unexpected severe side effects. Clofarabine combined with PEG‐ASP is safe and effective in the frontline treatment of ALL. A prospective, randomized trial is warranted to evaluate the antileukaemic efficacy of clofarabine versus HIDAC combined with PEG‐ASP.
Impact of smoking status and cumulative exposure on intravesical recurrence of upper tract urothelial carcinoma after radical nephroureterectomy
Authors: Xylinas Evanguelos , Kluth Luis A. , Rieken Malte , Lee Richard K. , Elghouayel Maya , Ficarra Vicenzo , Margulis Vitaly , Lotan Yair , Rouprêt Morgan , Martinez‐Salamanca Juan I. , Matsumoto Kazumasa , Seitz Christian , Karakiewicz Pierre I. , Zerbib Marc , Scherr Douglas S. , Shariat Shahrokh F. ,   UTUC Collaboration
Published: August 2013

Objective

To assess the impact of cigarette smoking status, cumulative smoking exposure, and time from cessation on intravesical recurrence (IVR) outcomes in patients treated with radical nephroureterectomy (RNU) for upper tract urothelial carcinoma (UTUC).

Patients and Methods

In all, 519 patients underwent RNU at five institutions. Smoking history included smoking status, quantity of cigarettes smoked per day (cpd), duration, and time from cessation.

The cumulative smoking exposure was categorised as light‐short‐term (≤19 cpd and ≤19.9 years), moderate (all combinations except light‐short‐term and heavy‐long‐term), and heavy‐long‐term (≥20 cpd and ≥20 years).

Univariable/multivariable cox regression analyses assessed the effects of smoking on IVR.

Results

In all, 190 patients (36%) never smoked; 205 (40%) and 125 (24%) were former and current smokers, respectively.

Among smokers, 42 (8%), 185 (36%), and 102 (20%) patients were light‐short‐term, moderate, and heavy‐long‐term smokers, respectively.

Within a median follow‐up of 37 months, 152 patients (29%) had IVR. Actuarial IVR‐free‐survival estimates (standard error) at 2, 5, and 10 years were 72 (2)%, 58 (3)%, and 51 (4)%, respectively.

In multivariable analyses, current smoking status, smoking intensity (≥20 cpd), smoking duration (≥20 years), and heavy‐long‐term smoking were associated with higher risk of IVR (all P ≤ 0.01).

Patients who quit smoking ≥10 years before RNU had better IVR outcomes than current smokers and those patients who quit smoking <10 years before RNU.

Conclusions

Cigarette smoking is significantly associated with IVR in patients treated with RNU for UTUC.

Current and heavy‐long‐term smokers have the highest risk of IVR.

Smoking cessation for >10 years before RNU seems to mitigate these detrimental effects.
Male circumcision wound healing in human immunodeficiency virus (HIV)‐negative and HIV‐positive men in Rakai, Uganda
Authors: Kigozi Godfrey , Musoke Richard , Kighoma Nehemiah , Watya Stephen , Serwadda David , Nalugoda Fred , Kiwanuka Noah , Nkale James , Wabwire‐Mangen Fred , Makumbi Frederick , Sewankambo Nelson K. , Gray Ronald H. , Wawer Maria J.
Published: August 2013

Objective

To assess completed wound healing after medical male circumcision (MMC) among human immunodeficiency virus (HIV)‐negative and HIV‐positive men with cluster of differentiation 4 (CD4) counts of <350 and ≥350 cells/mm3, as minimal data are available on the safety of MMC among HIV‐positive men with low CD4 counts.

Patients and Methods

In all, 262 HIV‐negative and 177 HIV‐positive consenting males aged ≥12 years accepted MMC using the dorsal slit procedure and were enrolled in the study.

Socio‐demographic and behavioural data and blood for HIV testing and CD4 counts were collected at baseline.

Participants were followed weekly to collect information on resumption of sex, condom use and both self‐reported and clinically assessed wound healing.

The proportions healed among HIV‐positive men were compared with HIV‐negative men. Time to complete wound healing was assessed by Kaplan–Meier survival analysis.

Results

There were no statistically significant differences in the proportion of men healed by HIV status.

At 4 weeks, the proportions healed were 85.9% in HIV‐negative men, 77.4% in HIV‐positive men with a CD4 count of ≥350 cells/mm3 and 87.1% in HIV‐positive men with a CD4 count of <350 cells/mm3.

The median time to healing was 4 weeks and did not vary by HIV or CD4 status.

All men had certified complete wound healing at 6 weeks after MMC. In all, 1.4% of HIV‐positive men with a CD4 count of <350 cells/mm3 resumed sex before healing, compared with 8.5% among HIV‐positive men with a CD4 count of ≥350 cells/mm3 (P = 0.052) and 7.8% (P = 0.081) among HIV‐negative men.

Conclusion

Inclusion of HIV‐positive men with low CD4 counts in MMC services is not deleterious to postoperative wound healing.
Training of European urology residents in laparoscopy: results of a pan‐European survey
Authors: Furriel Frederico T.G. , Laguna Maria P. , Figueiredo Arnaldo J.C. , Nunes Pedro T.C. , Rassweiler Jens J.
Published: August 2013

Objective

To assess the participation of European urology residents in urological laparoscopy, their training patterns and facilities available in European Urology Departments.

Materials and Methods

A survey, consisting of 23 questions concerning laparoscopic training, was published online as well as distributed on paper, during the Annual European Association of Urology Congress in 2012.

Exposure to laparoscopic procedures, acquired laparoscopic experience, training patterns, training facilities and motivation were evaluated.

Data was analysed with descriptive statistics.

Results

In all, 219 European urology residents answered the survey.

Conventional laparoscopy was available in 74% of the respondents' departments, while robotic surgery was available in 17% of the departments.

Of the respondents, 27% were first surgeons and 43% were assistants in conventional laparoscopic procedures. Only 23% of the residents rated their laparoscopic experience as at least ‘satisfactory’; 32% of the residents did not attend any course or fellowship on laparoscopy.

Dry laboratory was the most frequent setting for training (33%), although 42% of the respondents did not have access to any type of laparoscopic laboratory.

The motivation to perform laparoscopy was rated as ‘high’ or ‘very high’ by 77% of the respondents, and 81% considered a post‐residency fellowship in laparoscopy.

Conclusions

Urological laparoscopy is available in most European training institutions, with residents playing an active role in the procedure. However, most of them consider their laparoscopic experience to be poor.

Moreover, the availability of training facilities and participation in laparoscopy courses and fellowships are low and should be encouraged.
Dynamics of Polycomb chromatin domains under conditions of increased molecular crowding
Authors: Šmigová Jana , Juda Pavel , Bártová Eva , Raška Ivan
Published: August 2013

Background Information

A Polycomb (PcG) body is an orphan nuclear subcompartment characterised by accumulations of Polycomb repressive complex 1 (PRC1) proteins. However, seemingly contradictory reports have appeared that describe the PcG bodies either as protein‐based bodies in the interchromatin compartment or chromatin domains. In this respect, molecular crowding is an important factor for the assembly and stability of nuclear subcompartments. In order to settle this contradiction, crowding experiments, that represent a convenient model distinguishing between interchromatin and chromatin compartments, were carried out.

Results

In sucrose‐hypertonically induced crowding, we observed in U‐2 OS cells that PcG bodies disappeared, but persisted as nuclear domains characterised by accumulations of DNA. This phenomenon was also observed in cells hypertonically treated with sorbitol and NaCl. Importantly, the observed changes were quickly reversible after re‐incubation of cells in normal medium. We found that the PcG foci disappearance and the dissociation of PRC1 proteins (BMI1 and RING1a proteins) from chromatin were associated with their hyper‐phosphorylation. In addition, under hyper‐ and hypotonic conditions, the behaviour of the PcG bodies differed from that of the typical nucleoplasmic body.

Conclusion

PRC1 proteins accumulations do not represent a genuine nuclear subcompartment. The PcG body is a chromosomal domain, rather than a nucleoplasmic body.
Sediment fluxes and buffering in the post‐glacial Indus Basin
Authors: Clift P. D. , Giosan L.
Published: August 2013

The Indus drainage has experienced major variations in climate since the Last Glacial Maximum (LGM) that have affected the volumes and compositions of the sediment reaching the ocean since that time. We here present a comprehensive first‐order source‐to‐sink budget spanning the time since the LGM. We show that buffering of sediment in the floodplain accounts for ca. 20–25% of the mass flux. Sedimentation rates have varied greatly and must have been on average three times the recent, predamming rates. Much of the sediment was released by incision of fluvial terraces constructed behind landslide dams within the mountains, and especially along the major river valleys. New bedrock erosion is estimated to supply around 45% of the sedimentation. Around 50% of deposited sediment lies under the southern floodplains, with 50% offshore in large shelf clinoforms. Provenance indicators show a change of erosional focus during the Early Holocene, but no change in the Mid–Late Holocene because of further reworking from the floodplains. While suspended loads travel rapidly from source‐to‐sink, zircon grains in the bedload show travel times of 7–14 kyr. The largest lag times are anticipated in the Indus submarine fan where sedimentation lags erosion by at least 10 kyr.
Detection of novel paraja ring finger 2‐fer tyrosine kinase mRNA chimeras is associated with poor postoperative prognosis in non‐small cell lung cancer
Authors: Kawakami Masanori , Ishikawa Rie , Amano Yosuke , Sunohara Mitsuhiro , Watanabe Kousuke , Ohishi Nobuya , Yatomi Yutaka , Nakajima Jun , Fukayama Masashi , Nagase Takahide , Takai Daiya
Published: August 2013

Previously, we reported that the overexpression of fer tyrosine kinase (FER), a non‐receptor tyrosine kinase, is correlated with poor postoperative prognosis and cancer‐cell survival in non‐small cell lung cancer (NSCLC). In the present study, we further analyzed FER‐overexpressed NSCLC cases and identified various patterns of chimeric mRNAs, composed of paraja ring finger 2 (PJA2) and FER. We detected no genomic rearrangements between PJA2 and FER and attributed these chimeric mRNAs to alterations at the transcriptome level: i.e., trans‐splicing. Several chimeric patterns were detected concurrently in each patient, and the pattern sets varied among patients, although the pattern in which PJA2 exon 1 was fused to FER exon 3 (designated as Pe1‐Fe3 mRNA) was detected constantly. Therefore, in a wide screening for PJA2‐FER mRNAs in NSCLC, we focused on this chimeric pattern as a representative chimera. In analyses of 167 NSCLC samples, Pe1‐Fe3 mRNA was identified in about 10% of the patients, and the presence of chimeric mRNA was significantly correlated with a high expression level of parental FER mRNA. Furthermore, we found that the detection of Pe1‐Fe3 mRNA was correlated with poor postoperative survival periods in NSCLC, consistent with a previous finding in which FER overexpression was correlated with poor postoperative prognosis in NSCLC. This report is the first to suggest a correlation between chimeric mRNA and the expression level of parental mRNA. Furthermore, our findings may be clinically beneficial, suggesting that PJA2‐FER mRNAs might serve as a novel prognostic biomarker in NSCLC.
Heterogeneity of tumor endothelial cells
Authors: Hida Kyoko , Ohga Noritaka , Akiyama Kosuke , Maishi Nako , Hida Yasuhiro
Published: August 2013

Tumor blood vessels play important roles in tumor progression and metastasis. Thus, targeting tumor blood vessels is an important strategy for cancer therapy. Tumor endothelial cells (TECs) are the main targets of anti‐angiogenic therapy. Although tumor blood vessels generally sprout from pre‐existing vessels and have been thought to be genetically normal, they display a markedly abnormal phenotype, including morphological changes. The degree of angiogenesis is determined by the balance between the positive and negative regulating molecules that are released by tumor and host cells in the microenvironment. Reportedly, tumor blood vessels are heterogeneous with TECs differing from normal endothelial cells (in contrast to the conventional view). We recently compared characteristics of different TECs isolated from highly and low metastatic tumors. We found TECs from highly metastatic tumors had more proangiogenic phenotypes than those from low metastatic tumors. Elucidating the variety of TEC phenotypes and identifying TEC molecular signatures should lead to more complete understanding of the mechanisms of tumor progression, discovery of new therapeutic targets, and development of biomarkers. This review considers current studies on TEC heterogeneity and discusses the therapeutic implications of these findings.
Structural Bioinformatics‐Based Identification of EGFR Inhibitor Gefitinib as a Putative Lead Compound for BACE
Authors: Niu Mingshan , Hu Jin , Wu Sijin , Zhang Xiaoe , Xu Huaxi , Zhang Yunwu , Zhang Jie , Yang Yongliang
Published: August 2013

β‐secretase (BACE‐1) is a potential target for the treatment of Alzheimer's disease (AD). Despite its potential, only few compounds targeting BACE have entered the clinical trials. Herein, we describe the identification of Gefitinib as a potential lead compound for BACE through an integrated approach of structural bioinformatics analysis, experimental assessment and computational analysis. In particular, we performed ELISA and western analysis to assess the effect of Gefitinib using N2a human APP695 cells. In addition, we investigated the binding mechanism of Gefitinib with BACE through molecular docking coupled with molecular dynamics simulations. The computational analyses revealed that hydrophobic contact is a major contributing factor to the binding of Gefitinib with BACE. The results obtained in the study have rendered Gefitinib as a putative lead compound for BACE. Further optimization studies are warranted to improve its potency and pharmacological properties against BACE for potential AD treatment.
Child‐led research in the context of Australian social welfare practice
Authors: Michail Samia , Kellett Mary
Published: August 2013

This paper details the first child‐led research programme to be implemented in Australia in which children design and lead their own research about issues they identify. The programme was specifically adapted for children who were service users of a nongovernment organization that provides social welfare and support services to vulnerable children and their families, living in communities of the disadvantaged. The practitioner – researchers faced the expected challenges of power in child–adult relations pertinent to the status of children in a genuinely child‐led research endeavour. However, the paper details the additional challenges and responses required when conducting research in a practice environment and the successful adaptations that were used to meet these challenges. The positive findings of an independently commissioned programme evaluation raise important questions about the place and purpose of child‐led research within the field of children's social welfare practice.
The utilization of pre‐implantation genetic testing in the absence of governance: a real‐time experience
Authors: Farra C. , Nassar A. , Arawi T. , Ashkar H. , Monsef C. , Awwad J.
Published: August 2013

To create a diagnostic document describing the utilization of pre‐implantation genetic testing (PGT) in the absence of monitoring and regulation. Retrospective cohort study of couples undergoing PGT between 2004 and 2007 in Lebanon. The clinical indications for 192 PGT cycles performed during the study period were gender selection (96.3%), chromosomal aneuploidy (3.1%), and balanced translocation (0.5%). When gender selection was sought, the selection of a son was desired in 94.1% of cases. Of couples undergoing PGT for sex selection, 16.2% were childless, 8.6% had one child of the opposite gender, 28.1% had two same‐gender children, 29.7% had three same‐gender children, and 11.9% had four or more. Our findings demonstrate the morally questionable consequences of self‐regulated systems in which physicians are the sole gatekeepers of norms and ethics.
Importance of the National Petroleum Reserve–Alaska for Aquatic Birds
Authors: BART JONATHAN , PLATTE ROBERT M. , ANDRES BRAD , BROWN STEPHEN , JOHNSON JAMES A. , LARNED WILLIAM
Published: August 2013

We used data from aerial surveys (1992–2010) of >100,000 km2 and ground surveys (1998–2004) of >150 km2 to estimate the density and abundance of birds on the North Slope of Alaska (U.S.A.). In the ground surveys, we used double sampling to estimate detection ratios. We used the aerial survey data to compare densities of birds and Arctic fox (Vulpes lagopus), the major nest predator of birds, on the North Slope, in Prudhoe Bay, and in nearby areas. We partitioned the Prudhoe Bay oil field into 2 × 2 km plots and determined the relation between density of aquatic birds and density of roads, buildings, and other infrastructure in these plots. Abundance and density (birds per square kilometer) of 3 groups of aquatic birds—waterfowl, loons, and grebes; shorebirds; and gulls, terns, and jaegers—were highest in the National Petroleum Reserve–Alaska (NPRA) and lowest in the Arctic National Wildlife Refuge. Six other major wetlands occur in the Arctic regions of Canada and Russia, but the largest population of aquatic birds was in the NPRA. Aquatic birds were concentrated in the northern part of the NPRA. For example, an area that covered 18% of the NPRA included 53% of its aquatic birds. The aerial surveys showed that bird density was not lower and fox density was not higher in Prudhoe Bay than in surrounding areas. Density of infrastructure did not significantly affect bird density for any group of species. Our results establish that the NPRA is one of the most important areas for aquatic birds in the Arctic. Our results and those of others also indicate that oil production, as practiced in Prudhoe Bay, does not necessarily lead to substantial declines in bird density or productivity in or near the developed areas.

Prioridades para la Conservación de Aves en el Norte de Alaska
Cutaneous and systemic plasmocytosis
Authors: Wagner Gunnar , Rose Christian , Klapper Wolfram , Sachse Michael Max
Published: August 2013

Cutaneous and systemic plasmacytosis is a rare disorder observed mainly in Japanese that features an infiltration of mature plasma cells in various organ systems. In addition to the skin, lymph nodes and bone marrow are regularly affected. Laboratory tests show a polyclonal hypergammaglobulinemia. The cutaneous morphology is characterized by red to dark brown macules, papules and plaques a few centimeters in diameter, usually distributed symmetrically on the face, neck and back. Etiology and pathogenesis are not known. It is speculated that a reactive dysfunction of plasma cells may be triggered by various stimuli, such as interleukin 6. Treatment of cutaneous and systemic plasmacytosis is difficult. A standardized treatment concept does not yet exist. Topical corticosteroids and calcineurin inhibitors are mainly used.
Bayley‐II or Bayley‐III: what do the scores tell us?
Authors: Bos Arend F
Published: August 2013

This commentary is on the original article by Jary et al. on pages 1053–1059 of this issue.
Efficacy and safety of initial combination of DPP‐IV inhibitors and metformin versus metformin monotherapy in type 2 diabetes: a systematic review of randomized controlled trials
Authors: Gao W. , Dong J. , Liu J. , Li Y. , Liu F. , Yang L. , Zhou X. , Liao L.
Published: August 2013

Aims

We reviewed randomized controlled trials (RCTs) to compare the efficacy and safety of initial dipeptidyl peptidase‐IV (DPP‐IV) inhibitors and metformin combination therapy with equal‐dosage metformin monotherapy in type 2 diabetes.

Methods

We conducted a systematic review of English articles using MEDLINE and EMBASE. Search terms included randomized controlled trial, controlled clinical trial, random allocation, sitagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, duotogliptin and dipeptidyl peptidase IV inhibitor. Double‐blinded RCTs comparing DPP‐IV inhibitors initially combined with metformin and metformin monotherapy in non‐pregnant drug‐naive adults with type 2 diabetes were included for this study. Extraction of articles was performed by two authors using predefined data fields. Meta‐analysis was used when studies were homogeneous enough, and data were shown and not combined if no formal meta‐analysis was performed.

Results

Five RCTs met the inclusion criteria. By analysis of different outcomes, patients receiving initial combination of DPP‐IV inhibitors and metformin showed a greater reduction in haemoglobinA1c (HbA1c) from baseline [weighted mean difference (WMD), −0.55%; 95% confidence interval (CI), −0.63 to −0.46%], a higher rate of achieving target of HbA1c < 7% [risk ratio (RR), 1.55; 95% CI, 1.43–1.67], a significantly lower fasting plasma glucose (FPG) (WMD, −0.97 mmol/l; 95% CI, −1.26 to −0.68 mmol/l),while the initial combination therapy and monotherapy did not show a significant difference in incidence of total adverse events (AEs, 51.8 vs. 53.7%, respectively; RR, 0.96; 95% CI, 0.91–1.02), gastrointestinal AEs (18.2 vs. 19.4%, respectively; RR, 0.94; 95% CI, 0.82–1.07), drug‐related AEs (RR, 0.88; 95% CI, 0.74–1.03) and discontinuation due to AEs (RR, 0.85; 95% CI, 0.61–1.20). The following outcomes were not included for meta‐analysis: change from baseline in postprandial glycaemia, β‐cell function, insulin sensitivity and body weight as well as incidence of hypoglycaemia. The analyses of these trials revealed that the change from baseline of the postprandial glycaemia and index of β‐cell function were greater while the RRs for incidence of hypoglycaemia and body weight increase had no statistical significance.

Conclusions

Compared with equal‐dosage metformin monotherapy, the initial combination of metformin and DPP‐IV inhibitors were more effective in glycaemic control without additional risk of AEs, therefore it can be considered as a beneficial therapeutic regimen for drug‐naive type 2 diabetes patients.
The importance of Anguillids: a cultural and historical perspective introducing papers from the World Fisheries Congress
Authors: Kuroki Mari , Righton David , M. Walker Alan
Published: August 2013

Anguillid eels have been observed, studied, fished, traded and consumed by humans for centuries. As a consequence, societies have developed various cultural phenomena regarding cuisine, folklore, art, literature, legend. In recent years, however, some populations of eels have been in sharp decline across the globe, some species are now considered to be endangered, and there is an ever increasing need to share knowledge amongst the scientific, management and conservation community to protect these enigmatic fish, to reverse declines and elsewhere to prevent their occurrence. To facilitate this knowledge exchange, a congress session focussed on anguillid eels was held at the sixth World Fisheries Congress in May 2012 at the Edinburgh International Conference Centre. This special issue of Ecology of Freshwater Fish contains a number of the papers presented at the congress session, each focussed on a particular scientific problem. While the scientific study of eels is required to understand and manage eel resources, and to which end the majority of this volume is related, it is also necessary to take the cultural and social aspects of eels into account when considering how to ensure that this fascinating family of fishes has a sustainable future.
Inclusive Pedagogy in Light of Social Justice. Special Educational Rights and Inclusive Classrooms: on whose terms? A Field Study in Stockholm Suburbs
Authors: De Silva Nilani Ljunggren
Published: August 2013

The question of inclusive education is not straightforward. Despite all its good intentions, inclusive education, in practice faces numerous challenges today. This study analyses these challenges in the Swedish special education context. The author explores special educators’ experiences, possibilities and challenges when applying inclusive education. Findings reveal positive attitudes to the concept of inclusive classrooms. Nevertheless, teachers face more than a few grey areas that need to be put in place in order to achieve socially and cognitively inclusive classrooms.
Problematising Early School Leaving
Authors: Ross Alistair , Leathwood Carole
Published: August 2013

Early school leaving has been identified as a key policy priority across Europe. In this article, we critically discuss the underpinning assumptions and rationale for this policy focus, challenging the association that is made between early school leaving, economic growth and employment. We suggest that ESL is important, not because it is inhibiting growth or that it is responsible for high levels of youth unemployment, but because it helps to sustain and reproduce inequalities. We problematise the utilitarian conceptualisation of education and linear models of educational pathways that are embedded in this policy framework and critically discuss strategies that are proposed to address early school leaving. We argue that the key criteria for assessing such strategies should be the extent to which they meet social equity and social inclusion goals.
Further Education of Higher Education Graduates — the More, the Better?
Authors: Strauss Susanne , Leuze Kathrin
Published: August 2013

In times of rapid technological and organisational change, it is argued that lifelong further education becomes more and more important for labour market success. Especially in labour market segments for the highly qualified, it is essential to constantly update one's qualifications. This is reflected in the finding that graduates with tertiary education are closely involved in further training measures at the beginning of their life courses. Almost all take part in at least one further training measure in the first five years after graduation. The further education strategies of higher education graduates, however, vary greatly in terms of frequency of participation, duration of measures, financing of the measure and the type of skills acquired. Using aGerman graduate panel which traces a sample of graduates up to five years after they obtained their degree in 1997 (HIS Absolventenpanel), we analyse which of these strategies are most successful in terms of wages. Using random effect panel models, we find — controlling for a variety of other factors — that the frequency of participation in further education only has a significant positive influence on male graduates' wages. Moreover, it is mainly measures paid exclusively by the employer and courses directed at personality development, i.e. management skills, which have substantial wage premiums.