bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 34KSNPgenotyping array forPopulus trichocarpa: Design, application to the study of natural populations and transferability to otherPopulusspecies
Authors: Geraldes A. , DiFazio S. P. , Slavov G. T. , Ranjan P. , Muchero W. , Hannemann J. , Gunter L. E. , Wymore A. M. , Grassa C. J. , Farzaneh N. , Porth I. , McKown A. D. , Skyba O. , Li E. , Fujita M. , Klápště J. , Martin J. , Schackwitz W. , Pennacchio C. , Rokhsar D. , Friedmann M. C. , Wasteneys G. O. , Guy R. D. , El‐Kassaby Y. A. , Mansfield S. D. , Cronk Q. C. B. , Ehlting J. , Douglas C. J. , Tuskan G. A. 
Published: January 2013

AbstractGenetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost‐effective solution. Herein we report on the design and performance of aSNPgenotyping array forPopulus trichocarpa(black cottonwood). This genotyping array was designed withSNPs pre‐ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of theSNPs on the array (539) was selected based on patterns of variation among theSNPdiscovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.
Molecular identification of dipteran pests (Diptera: Sciaroidea) from shiitake mushroom
Authors: Shin Seunggwan , Jung Sunghoon , Lee Heungsik , Lee Seunghwan 
Published: January 2013

AbstractOn shiitake farms, mycophagous maggots can cause serious damage by preventing formation of the fruiting body. Recently, these pests have significantly reduced shiitake production in Korea. However, larvae and female adults cannot be identified due to their lack of morphological characteristics. Therefore, farmers and applied entomologists are unable to determine which species is the primary cause of the shiitake damage. In this study, mycophagous flies (colonized larvae) were collected from damaged shiitake farms and subsequently identified by matching identified males with the cytochrome c oxidase subunit I (COI) sequences from the larvae. Divergences of the COI sequences among the species discriminated the clusters clearly, and the mycophagous pests were identified as Camptomyia corticalis and C. heterobia. Interestingly, these two species coexisted under the bark of shiitake oak bed logs.
msap: a tool for the statistical analysis of methylation‐sensitive amplified polymorphism data
Authors: Pérez‐Figueroa A. 
Published: January 2013

ABSTRACTIn this study msap, an R package which analyses methylation‐sensitive amplified polymorphism (MSAP or MS‐AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user‐friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user‐defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments.msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses.
Prasugrel Reduces Agonists′ Inducible Platelet Activation and Leukocyte–Platelet Interaction more efficiently than Clopidogrel
Authors: Gremmel Thomas , Eslam Roza Badr , Koppensteiner Renate , Lang Irene M. , Panzer Simon 
Published: January 2013

SummaryAimsThe antiplatelet effects of clopidogrel and prasugrel have mainly been compared using different platelet reactivity tests. Further, data on the impact of both drugs on thrombin‐inducible platelet activation are scarce. We therefore investigated the influence of clopidogrel and prasugrel on different flow cytometric parameters of platelet activation as well as on platelet function assessed by leukocyte–platelet interaction.MethodsBaseline, ADP and thrombin receptor‐activating peptide (TRAP)‐6 inducible P‐selectin expression, activation of glycoprotein (GP) IIb/IIIa and monocyte–platelet aggregate (MPA) formation were determined by flow cytometry in 84 clopidogrel‐ and 21 prasugrel‐treated patients undergoing percutaneous coronary intervention with stent implantation.ResultsBaseline expressions of P‐selectin and activated GPIIb/IIIa did not differ significantly between clopidogrel‐ and prasugrel‐treated patients (both P > 0.2). After activation with ADP or TRAP‐6, patients with clopidogrel therapy exhibited significantly higher platelet surface expressions of P‐selectin and activated GPIIb/IIIa than prasugrel‐treated patients (all P ≤ 0.001). Further, high P‐selectin and high GPIIb/IIIa were significantly more frequent in clopidogrel‐treated patients than in patients on prasugrel therapy (all P = 0.01). Likewise, the formation of MPA without addition of agonists did not differ significantly between patients receiving clopidogrel and patients on prasugrel therapy (P = 0.2). After activation with ADP or TRAP‐6, clopidogrel‐treated patients showed a significantly more pronounced formation of MPA than patients‐receiving prasugrel (both P = 0.02).ConclusionsPrasugrel reduces ADP and TRAP‐6 inducible platelet activation, and leukocyte–platelet interaction more efficiently than clopidogrel.
Age and Sex Effects on the Single‐ and Multiple‐Dose Safety and Pharmacokinetics of the New Renin Inhibitor ACT‐178882
Authors: Dingemanse Jasper , Nicolas Laurent 
Published: January 2013

SummaryAimTo investigate the effect of age and sex on the single‐ and multiple‐dose safety and pharmacokinetics of ACT‐178882, a new direct renin inhibitor.MethodsIn the single‐dose, open‐label part of the study, healthy young and elderly male and female subjects received a dose of 300 mg ACT‐178882. In the multiple‐dose, double‐blind, placebo‐controlled part of the study, healthy elderly male and female subjects received ACT‐178882 (300 or 600 mg) or placebo once‐a‐day for 14 days.ResultsMild headache and diarrhea were the most common adverse events in the single‐ and multiple‐dose parts, respectively. The frequency of diarrhea increased dose dependently, and no placebo subjects reported this adverse event. Administration of ACT‐178882 did not result in any clinically relevant changes in ECG, vial signs, clinical laboratory, body weight, or physical examination. In the single‐dose part and independent of sex, values for Cmax and AUC0–∞ were about 85% higher in elderly compared with young subjects, and t1/2 was about 5 h longer (29.3 vs. 24.1 h). In both age groups, plasma ACT‐178882 concentrations were slightly higher in female versus male subjects. Following multiple‐dose administration to elderly subjects, accumulation of ACT‐178882 was moderate, about 1.8‐fold, t1/2 was unchanged as compared with single‐dose administration, sex effects were minimal, and the increase in the exposure with increasing dose appeared less than dose proportional.ConclusionOverall, single‐ and multiple‐dose administration of ACT‐178882 was well tolerated. No dose adaptation based on sex is necessary, whereas a dose reduction based on age could be considered.
Prioritizing conservation areas around multispecies bat colonies using spatial modeling
Authors: Rainho A. , Palmeirim J. M. 
Published: January 2013

AbstractBats and other vertebrates form large colonies concentrating key populations of multiple endangered species. Their foraging ranges are of critical importance for the colony but can be too vast to preserve in full extent. We evaluated an approach to prioritize areas within this range that conciliates the distinct needs of various species.Our model colony was a large cave‐bat nursery harboring Rhinolophus mehelyi, Myotis myotis and Miniopterus schreibersii located in Southern Portugal. With radio‐tracking data of foraging bats and spatially explicit modeling, we generated habitat suitability maps for each species. Models incorporated both habitat variables and distance to the roost. The resulting maps were then used separately or in combinations to identify the areas with greatest multispecies conservation value.The best results were obtained by combining individual suitabilities in a single value, weighting each species by its threat risk. Although the overall range of the colony was very extensive, this approach identified the areas that had most multispecies value; more than half of the foraging sites are included in the best 13% of the range, and adding the next best 12% includes almost all sites of the most threatened study species, R. mehelyi. The efficiency of the prioritization can be evaluated not only for the species ensemble, but also for individual species.The concentration of most multispecies conservation value in a small area is partly due to the importance of distance to roost as a determinant of foraging habitat selection in all species, so this factor is essential in suitability models used for prioritization. This prioritization process successfully minimizes the amount of land required for protection, while maximizing the quality of the habitat to protect. Such prioritizations should spur the preservation of foraging areas of large multispecies colonies, thus improving the chances of survival of populations of great conservation value.
Protected areas and insect conservation: questioning the effectiveness ofNatura 2000 network for saproxylic beetles inItaly
Authors: D'Amen M. , Bombi P. , Campanaro A. , Zapponi L. , Bologna M. A. , Mason F. 
Published: January 2013

Read the Commentaries on this Feature Paper:Institutional vertebratism hampers insect conservation generally; not just saproxylic beetle conservation;Knowledge gaps in protected area effectivenessResponse from the authors:Possible directions in the protection of the neglected invertebrate biodiversity
Aortic Surgery After Previous Procedure of Congenital Aortic Stenosis
Authors: Tirilomis Theodor , Coskun K. Oguz , Popov Aron‐Frederik , Ruschewski Wolfgang 
Published: January 2013

AbstractIrrespective of previous procedure in congenital aortic stenosis, aortic surgery later in life may be indicated. The aim of the present study was the analysis of indications, risks, and outcomes of aortic surgery after previous aortic valve procedure. The data of patients who underwent aortic surgery after previous treatment of congenital aortic stenosis in a 10‐year period (from 2000 to 2009) were retrospectively analyzed. Thirty‐two patients (23 male and 9 female) underwent redo aortic surgery. The mean age at surgery was 13.5 ± 11.3 years. Seventeen patients had undergone initial aortic balloon valvuloplasty (BVP) and 15 patients open commissurotomy (COM). Nine cases had undergone the primary procedure at neonatal age and two patients had undergone cardiac surgery before the initial aortic valve procedure. Seven of the patients with previous COM (43.8%) had undergone concomitant surgery along with initial commissurotomy. A reintervention within the first year after the primary procedure was performed in seven patients (seven after BVP and none after COM; P < 0.05). The interval between the last intervention and the first redo aortic surgery was 7.5 ± 9.5 years (3.1 ± 3.5 years after BVP vs. 12.5 ± 11.7 years after COM; P < 0.05). A second redo surgery was performed in nine patients (four after initial BVP and five after COM). Congenital aortic stenosis is very often presented in combination with additional pathologies. These concomitant diseases along with the underlying disease give the indication for reoperation. Reinterventions are more often indicated after primary BVP. Long follow‐up in specialized centers is mandatory.
Pediatric Single‐Lumen Cannula Venovenous Extracorporeal Membrane Oxygenation: A French Center Experience
Authors: Léger Pierre‐Louis , Guilbert Julia , Isambert Ségolène , Le Saché Nolwenn , Hallalel Fazia , Amblard Alain , Chevalier Jean‐Yves , Renolleau Sylvain 
Published: January 2013

Abstract  Single‐lumen cannula venovenous (VV) extracorporeal membrane oxygenation (ECMO) is a special extracorporeal life support (ECLS) technique used for neonatal and pediatric refractory hypoxemia. This is an alternative flow rate ECLS that consists of successive clamping on the drainage and the injection lines. Currently, the Armand‐Trousseau's pediatric intensive care unit remains the only pediatric ECMO center proposing this partial assistance. This article details a technical note and a retrospective analysis of our experience in refractory hypoxemia. The retrospective study, from 2007 to 2011, included all pediatric and neonatal patients treated by single‐lumen cannula VV ECMO. The study was focused on pre‐ECMO patient characteristics and complications during ECMO course. During the last 5 years, 67 pediatric patients were assisted by this single‐lumen cannula VV ECMO. Sixty‐one patients (91%) were newborns. Thirty‐nine patients presented with meconium aspiration syndrome (58%), which was the most frequent etiology. Before cannulation, mean oxygenation index (OI) was 32 ± 11, alveolar‐arterial oxygen difference was 604 ± 47 mm Hg, and partial pressure arterial oxygen/fraction inspired oxygen ratio was 59.2 ± 35.8. Forty‐eight patients (72%) presented pulmonary hypertension, and 66 patients were treated by nitric oxide (98%). Fifty patients (75%) were treated by vasopressors or inotropic drugs. Average duration of ECMO was 13.2 ± 7.8 days. There were forty‐six survivors (69%). The worst prognosis was for respiratory syncytial virus pneumonia. Complications like acute renal injury and hematologic and transfusion acts were not so different than those observed in classical ECMO techniques. Nevertheless, 19 patients presented a stroke (28% of the overall population), but this high rate did not seem to be due to the ECLS technique used. Single‐lumen cannula VV ECMO is a partial and efficient ECMO support. Our experience shows that this technique is as efficient and less invasive than two cannulas ECMO. The single‐lumen cannula VV ECMO is a simple and safe ECLS support used for neonatal or pediatric refractory hypoxemia. Because this is a partial assistance, it is a promising ECLS support.
Myocardial Protection in Pediatric Cardiac Surgery
Authors: Turkoz Rıza 
Published: January 2013

AbstractThe combination of hypothermia and potassium cardioplegic arrest has become the most common method of myocardial protection in the evolution of myocardial protection. This review focuses on myocardial protection in pediatric cardiac surgery. In the 1980s, blood was added to cardioplegia solution in order to supply the myocardium with oxygen, nutrients, and for buffering purposes. Similar myocardial protection methods have been used in adult and pediatric groups for many years. However, the immature heart in the pediatric group differs in many ways from the mature hearts in adults. Low cardiac output is more often observed in pediatric patients. Most cardiac operations are performed under cardioplegic arrest in pediatric cardiac surgery. Today there are a lot of different types of cardioplegia solutions and methods used in pediatric cardiac surgery. Soon after normothermic perfusion was used in the adult cardiac surgery in the beginning of the 1990s, normothermic perfusion and cardioplegia began to be used in pediatric myocardial protection. Myocardial protection is more challenging in particular cases such as: (i) long and complex cases in which repetitive cardioplegia administration through the aortic root is difficult; (ii) newborn patients; and (iii) cases with preoperative damaged myocardium. If the mortality and morbidity rates of the centers in complex and long procedures are higher than the reported rates in literature, the myocardial protection method must be suspected and reorganized.
Low‐Output Is Not the Cause of Death of Neonatal Piglets Early After Cardiopulmonary Bypass
Authors: Tirilomis Theodor , Bensch Marc , Nolte Lars , Steinke Katja , Schoendube Friedrich A. 
Published: January 2013

AbstractThe mortality rate of neonatal piglets after heart surgery is high. Searching for a possible explanation for the death of neonatal piglets early after cardiopulmonary bypass, we analyzed hemodynamic parameters regarding survival and non‐survival. Initially, 10 neonatal piglets (younger than 7 days) were connected to cardiopulmonary bypass (CPB). The mean body weight was 2.98 ± 0.44 kg. Exposure of the heart was performed through a median sternotomy. After connection to the CPB, the piglets were cooled to 32°C core temperature before the ascending aorta was cross‐clamped and the heart arrested (90 min). Thereafter, piglets were re‐warmed to 37°C and separated from CPB. During follow‐up, the piglets did not receive inotropic support or vasopressors. Piglets who survived at least 2 h after termination of CPB were included in the study for further data analysis (n = 9). Five piglets died 2.5 to 4.0 h (median: 3.5 h) after CPB; these piglets formed the non‐survivors group. Four animals survived the complete follow‐up of 6 h after CPB and formed the survivors group. Regarding contractility (dP/dtmax, dP/dtmax/P, and wall thickening) there were not statistically significant differences between the groups. Non‐survivors showed prolonged decrease of mean arterial pressure of more than 20% of baseline values, corresponding with a value of below 30 mm Hg. In conclusion, the death of neonatal piglets early after cardiopulmonary bypass was not determined by low output.
Reduction of Driveline Infections Through Doubled Driveline Tunneling of Left Ventricular Assist Devices
Authors: Fleissner Felix , Avsar Murat , Malehsa Doris , Strueber Martin , Haverich Axel , Schmitto Jan D. 
Published: January 2013

AbstractThe durability of ventricular assist device (VAD) therapy improved steadily over the past years. However, driveline infections remain a challenge. To test whether an improved surgical implantation technique may lower the incidence of infections, we analyzed all patients receiving a VAD implantation in the years 2008 and 2009 (group 1) and compared them with all patients who received a VAD in 2011 (group 2) after we changed our implantation method. The new technique involves tunneling of the driveline into the fascia of the musculus rectus abdominis, resulting in a longer, intrafascial run to achieve a better resistance against ascending infections. We retrospectively analyzed 40 patients in group 1 and 41 patients in group 2. One year after implantation, the infection rate was markedly reduced (22.5% [n = 9] group 1 vs. 4.9% [n = 2] group 2, P < 0.001) by the new implantation method. There was, however, no significant improvement in overall mortality. The Cox regression model identified the implantation method as an independent risk factor for 1 year after implantation driveline infection (P < 0.05). In conclusion, the new tunneling technique marks a great leap forward in long‐term VAD treatment. However, overall mortality remains high and needs further improvement.
Meta‐analysis: the association of hepatitis B virus genotypes and hepatocellular carcinoma
Authors: Wong G. L.‐H. , Chan H. L.‐Y. , Yiu K. K.‐L. , Lai J. W.‐Y. , Chan V. K.‐K. , Cheung K. K.‐C. , Wong E. W.‐N. , Wong V. W.‐S. 
Published: January 2013

SummaryBackgroundA meta‐analysis on the risk of hepatocellular carcinoma (HCC) among hepatitis B virus (HBV) genotypes is warranted as the current data are conflicting.AimTo investigate the relative risk of HCC among the four major HBV genotypes (A–D).MethodsA meta‐analysis was performed based on literature search from electronic databases and bibliography between 1950 and 2012. All abstracts with keywords ‘hepatitis B’, ‘hepatocellular carcinoma’ and ‘genotype’ were screened. Studies were included if they reported HBV genotype as an exposure and HCC as an outcome.ResultsNine hundred and eighty‐eight abstracts were found through literature search, among them 43 studies were eligible for this meta‐analysis. A total of 14 545 patients with an average age of 43 years were included; 71% were male patients and 17% had cirrhosis. In 33 studies, HCC was found in 1541/6060 (25%) genotype C vs. 550/4417 (12%) genotype B HBV‐infected patients [odds ratio (OR) = 2.05, 95% confidence interval (CI) = 1.52–2.76, P < 0.001]. No difference in the risk of HCC was found among genotype A (71/517, 14%) vs. genotype D (170/1506, 11%) HBV‐infected patients in 14 studies (OR = 0.94, 95% CI = 0.67–1.32). In 10 studies, the risk of HCC was also found higher among genotype C (498/1659, 30%) than genotype A&D (103/1403, 7%) HBV‐infected patients (OR = 2.34, 95% CI = 1.63–3.34, P < 0.001). Subgenotype Ce and Cs HBV‐infected patients had similar risk on HCC (OR = 1.13, 95% CI = 0.76–1.67, P = 0.54). On funnel plot analysis, there was no significant publication bias in all comparisons.ConclusionGenotype C hepatitis B virus is associated with a higher risk of hepatocellular carcinoma than other major hepatitis B virus genotypes.