bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of 11 single‐locus and seven multilocusDNAbarcodes inLamiumL. (Lamiaceae)
Authors: Krawczyk K. , Szczecińska M. , Sawicki J. 
Published: October 2013

AbstractThe aim of this work was to evaluate the suitability of selectedDNAregions in the barcoding of plants, based on the species belonging to the genusLamium(Lamiaceae). For this purpose, nine chloroplast barcodes, that is,accD,matK, rbcL, rpoA,rpoB,rpoC1,rpoC2,trnH‐psbA,trnL‐trnF, as well asITSnuclear region, and intron of mitochondrialnad5gene were tested. Among the single‐locus barcodes, most effective in the identification ofLamiumspecies was thetrnH‐psbAspacer andmatKgene. The high level of variability and resolving power was also observed in the case ofrpoAandrpoC2genes. Despite the high interspecies variability ofITSregion, it turned out to be inapplicable inLamiumidentification. An important disadvantage ofITSas a barcode is a limitation of its use in polyploid plants, samples contaminated with fungal material or samples with partially degradedDNA. We have also evaluated five‐two‐locus and two‐three‐locus barcode regions created from a combination of most effective single loci. The best‐performing barcode combinations werematK + trnH‐psbAandmatK + rpoA. Both of them had equally high discriminative power to identifyLamiumspecies.
Practical Considerations in the Use of Novel Oral Anticoagulants for Stroke Prevention in Nonvalvular Atrial Fibrillation
Authors: Deitelzweig Steven 
Published: October 2013

SummaryAtrial fibrillation (AF) is a highly prevalent cardiac arrhythmia associated with an increased risk of stroke. The role of anticoagulation therapy in the prevention of thrombosis and stroke is of critical importance for patients with AF. Limitations with vitamin K antagonists (VKAs), the current standard of care, have led to the development of novel oral anticoagulants (NOACs) that target either thrombin (dabigatran etexilate) or activated factor X (rivaroxaban, apixaban, and edoxaban). In comparison with traditional VKAs such as warfarin, these NOACs offer several pharmacologic advantages, including rapid onset of action, no significant food interactions, low potential for drug–drug interactions, and no requirement for routine coagulation monitoring. Completed phase‐III clinical trials have demonstrated the therapeutic potential of dabigatran, rivaroxaban, and apixaban in comparison with warfarin for stroke prevention in patients with nonvalvular AF (NVAF). While the future utility of NOACs in preventing stroke in patients with NVAF looks promising, several practical issues, including the current lack of a reversal strategy and use of these agents in older patients with renal dysfunction, must be considered. Clinician and patient understanding of such issues will be important for the safe and effective use of NOACs.
SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons
Authors: Liu Shanlin , Li Yiyuan , Lu Jianliang , Su Xu , Tang Min , Zhang Rui , Zhou Lili , Zhou Chengran , Yang Qing , Ji Yinqiu , Yu Douglas W. , Zhou Xin 
Published: October 2013

Summary

Metabarcoding of mixed arthropod samples for biodiversity assessment has mostly been carried out on the 454 GS FLX sequencer (Roche, Branford, Connecticut, USA), due to its ability to produce long reads (≥400 bp) that are believed to allow higher taxonomic resolution. The Illumina sequencing platforms, with their much higher throughputs, could potentially reduce sequencing costs and improve sequence quality, but the associated shorter read length (typically <150 bp) has deterred their usage in next‐generation‐sequencing (NGS)‐based analyses of eukaryotic biodiversity, which often utilize standard barcode markers (e.g. COI, rbcL, matK, ITS) that are hundreds of nucleotides long.

We present a new Illumina‐based pipeline to recover full‐length COI barcodes from mixed arthropod samples. Our new assembly program, SOAPBarcode, a variant of the genome assembly program SOAPdenovo, uses paired‐end reads of the standard COI barcode region as anchors to extract the correct pathways (sequences) out of otherwise chaotic ‘de Bruijn graphs’, which are caused by the presence of large numbers of COI homologs of high sequence similarity.

Two bulk insect samples of known species composition have been analysed in a recently published 454 metabarcoding study (Yu et al. 2012) and are re‐analysed by our analysis pipeline. Compared to the results of Roche 454 (c. 400‐bp reads), our pipeline recovered full‐length COI barcodes (658 bp) and 17–31% more species‐level operational taxonomic units (OTUs) from bulk insect samples, with fewer untraceable (novel) OTUs. On the other hand, our PCR‐based pipeline also revealed higher rates of contamination across samples, due to the Illumina's increased sequencing depth. On balance, the assembled full‐length barcodes and increased OTU recovery rates resulted in more resolved taxonomic assignments and more accurate beta diversity estimation.

The HiSeq 2000 and the SOAPBarcode pipeline together can achieve more accurate biodiversity assessment at a much reduced sequencing cost in metabarcoding analyses. However, greater precaution is needed to prevent cross‐sample contamination during field preparation and laboratory operation because of greater ability to detect non‐target DNA amplicons present in low‐copy numbers.
Using social structure to improve mortality estimates: an example with sperm whales
Authors: Whitehead Hal , Gero Shane 
Published: October 2013

Summary

Estimates of mortality are fundamental to studies of population ecology and assessments of conservation status. Mortality is frequently estimated using individual identifications by means of mark–recapture methods. These estimates become biased with heterogeneity in identification and especially if patterns of heterogeneity change with time.

If animals are social, then survival may be inferred from the identifications of social partners. We produce a likelihood model for estimating mortality using such social data.

We show using simulation that this method can produce less biased and more precise estimates of mortality than standard methods when individuals are almost always identified with associates, and when there are time‐varying patterns of heterogeneity in identifiability. The method seems little affected by some change in social affiliations or by growth or decline in population size. SEs and confidence intervals of mortality estimates can be estimated using likelihood methods. We apply the method to data from a population of sperm whales (Physeter macrocephalus) in the eastern Caribbean, obtaining estimates that are more precise and probably less biased than those from other methods.

The method should be useful in improving mortality estimates for social species.
Systematic study of Duadicus Dallas, 1851 (Insecta: Hemiptera: Heteroptera: Acanthosomatidae: Blaudusinae: Blaudusini), including the description of a new species from Western Australia
Authors: Wang Xiao‐Jing , Liu Guo‐Qing , Cassis Gerasimos 
Published: October 2013

AbstractA new species of the acanthosoamtid genus Duadicus Dallas is described from Australia: D. namyatovae sp. nov., which is endemic to Western Australia. The type species D. pallidus is redescribed including the first detailed description of the male and female genitalia. Digital images, scanning electron micrographs and illustrations of the diagnostic characters are provided for both species. Host plant associations for both species are given, with preferences for species belonging to Melaleuca.
Zambia's input subsidy programs
Authors: Mason Nicole M. , Jayne T.S. , Mofya‐Mukuka Rhoda 
Published: October 2013

AbstractOver the last decade, subsidies for fertilizer and hybrid maize seed have re‐emerged as a cornerstone of the Government of the Republic of Zambia's (GRZ's) agricultural development and poverty reduction strategies. This article reviews the Farmer Input Support Programme (FISP) and other GRZ input subsidy programs since structural adjustment. It then synthesizes existing and presents new empirical evidence on the programs’ targeting outcomes and effects. Results suggest that although 73% of smallholder households cultivate less than 2 hectares of land, and that these households constitute 78% of the smallholder farms below the US$1.25/capita/day poverty line, the majority (55%) of FISP fertilizer goes to households that cultivate larger areas. Other factors constant, wealthier households receive more subsidized inputs. Subsidized fertilizer promotes maize intensification and extensification (at the expense of fallow land), but an additional kg of subsidized fertilizer only raises maize output by 1.88 kg on average. As a result of low maize–fertilizer response rates, poor targeting, crowding out, and diversion of fertilizer intended for the program, financial benefit–cost ratios for FISP fertilizer are well below one. The article concludes with recommended reforms to FISP, including that it be downsized and the savings invested in known drivers of pro‐poor agricultural growth.
How do fertilizer subsidy programs affect total fertilizer use in sub‐Saharan Africa? Crowding out, diversion, and benefit/cost assessments
Authors: Jayne T.S. , Mather David , Mason Nicole , Ricker‐Gilbert Jacob 
Published: October 2013

AbstractA major determinant of input subsidy programs’ effects on the achievement of national policy goals is the extent to which they raise total fertilizer use. This study synthesizes recent literature on how the new generation of targeted input subsidy programs has affected national fertilizer use after accounting for crowding effects, and derives benefit–cost (BC) estimates of the fertilizer subsidy programs for Kenya, Malawi, and Zambia after accounting for crowding out and diversion. We highlight two major findings. First, accounting for the illicit diversion of program fertilizer can profoundly influence estimates of how fertilizer subsidy programs affect total fertilizer use and program impacts. Given recent evidence that 33% or more of total program fertilizer may be diverted before being received by intended beneficiary farmers, the failure to account for program diversion is shown to overestimate the contribution of the subsidy programs to national fertilizer use by 67.3% in the case of Malawi, by 61.6% for Zambia, and by 138.0% for Kenya. The second major finding is that the incremental value of maize output produced from these subsidy programs is considerably less than their costs in most years, except under unusually high maize price assumptions. Conventional BC analyses that do not account for crowding out and diversion may seriously overestimate the benefits of input subsidy programs. Greater attention to program design and implementation details to reduce problems of crowding out and diversion can substantially raise the returns to such programs.
Cutting Edge: IL‐10‐Producing Regulatory B Cells in Early Human Pregnancy
Authors: Rolle Luise , Memarzadeh Tehran Maryam , Morell‐García Anselm , Raeva Yanitsa , Schumacher Anne , Hartig Roland , Costa Serban‐Dan , Jensen Federico , Zenclussen Ana Claudia 
Published: October 2013

ProblemThe function of IL‐10 producing regulatory B cells (Breg) during gestation is unknown. Here, we aimed to understand their participation in early pregnancy.MethodCD19+CD24hiCD27+B cell frequency, measured by flow cytometry, increased with pregnancy onset but not in the case of spontaneous abortions.ResultsB cells from non‐pregnant women cultured with serum from normal pregnant women produced higher IL‐10 levels than those cultured with serum from spontaneous abortion patients or autologous serum. CD19+‐activated B cells from pregnant women strongly suppressed TNF‐a production by CD4+T cells when cocultured. We identified hCG as an important factor regulating the number and function of Breg during pregnancy.ConclusionsBreg emerge as important players in pregnancy; they suppress undesired immune responses from maternal T cells and are therefore important for tolerance acquisition.
Postpartum voiding dysfunction: Identifying the risk factors
Authors: Buchanan Julie , Beckmann Michael 
Published: October 2013

BackgroundPostpartum urinary retention (PPUR) (also known as voiding dysfunction) is a common problem, defined as the inability to completely void after giving birth. If voiding dysfunction is not recognised, bladder overdistension can lead to denervation, detrusor atony and prolonged voiding dysfunction.AimTo describe the incidence of PPUR amongst postpartum women undergoing routine bladder scanning and to identify the factors that lead to postpartum voiding dysfunction.MethodsA retrospective analysis of all postpartum women at Mater Health Services, Brisbane between February and December 2012 was undertaken. Routinely collected postvoid residual bladder volumes (PVRBV) were reported using a bladder scanner at four and six hours and two to three days postbirth or following removal of an indwelling catheter (IDC). The characteristics of women with or without increased PVRBV were analysed.ResultsPostvoid residual bladder volumes at four‐hours postbirth/removal of IDC were available for 5558 women of whom 281 (5.1%) had a residual volume measured >150 mL. Obstetric factors explored included mode of birth, method of analgesia or anaesthesia, duration of labour, degree of perineal trauma, birth weight, gestation, parity, maternal age and body mass index. After controlling for confounders, nulliparity (aOR 1.53; 95% CI 1.05–2.26), birth by caesarean section (aOR 2.21; 95% CI 1.10–4.41) and 3rd/4th degree perineal trauma (aOR 2.01; 95% CI 1.09–3.72) were significant independent predictors of PPUR.ConclusionFollowing the introduction of a protocol of timed voiding and routine measurement of PVRBV after birth/removal of IDC, PPUR is uncommon. Adopting a risk‐factor‐based approach to PVRBV screening is not supported by these data.
Staphylococcus aureus enterotoxin‐specific IgE is associated with asthma in the general population: a GA2LEN study
Authors: Tomassen P. , Jarvis D. , Newson R. , Van Ree R. , Forsberg B. , Howarth P. , Janson C. , Kowalski M. L. , Krämer U. , Matricardi P. M. , Middelveld R. J. M. , Todo‐Bom A. , Toskala E. , Thilsing T. , Brożek G. , Van Drunen C. , Burney P. , Bachert C. 
Published: October 2013

AbstractBackgroundSpecific IgE to Staphylococcus aureus enterotoxins (SE‐IgE) has been associated with asthma. In the general population, we aimed to determine the prevalence of and risk factors for serum SE‐IgE and to examine the association with asthma.MethodsA postal questionnaire was sent to a random sample of adults in 19 centers across Europe. A random sample of respondents was invited for clinical examination upon which they answered a questionnaire, underwent skin prick tests (SPTs) for common aeroallergens, and provided blood for measurement of total IgE and SE‐IgE. Risks were analyzed within centers using weighted logistic regression, and overall estimates calculated using fixed‐effects meta‐analysis.Results2908 subjects were included in this analysis. Prevalence of positive SE‐IgE was 29.3%; no significant geographic variation was observed. In contrast to positive skin prick tests, SE‐IgE was more common in smokers (<15 pack‐year: OR 1.11, P = 0.079, ≥15 pack‐year: OR 1.70, P < 0.001), and prevalence did not decrease in older age‐groups or in those with many siblings. Total IgE concentrations were higher in those with positive SE‐IgE than in those with positive SPT. SE‐IgE was associated with asthma (OR 2.10, 95% confidence interval [1.60–2.76], P = 0.001) in a concentration‐dependent manner. This effect was independent of SPT result and homogeneous across all centers.ConclusionsWe report for the first time that SE‐IgE is common in the general population throughout Europe and that its risk factors differ from those of IgE against aeroallergens. This is the first study to show that SE‐IgE is significantly and independently associated with asthma in the general population.
A randomised prospective trial of intra‐operative oesophageal Doppler‐guided fluid administration in major gynaecological surgery
Authors: McKenny M. , Conroy P. , Wong A. , Farren M. , Gleeson N. , Walsh C. , O'Malley C. , Dowd N. 
Published: October 2013

SummaryIntra‐operative oesophageal Doppler monitor‐guided fluid management has been associated with improved postoperative length of hospital stay and morbidity in gastrointestinal and orthopaedic surgery. We designed a randomised controlled trial to test the hypothesis that this approach to intra‐operative fluid management in major elective open gynaecological surgery would shorten the length of postoperative stay, defined as time to readiness for hospital discharge. Postoperative morbidity was evaluated as a secondary outcome. The oesophageal Doppler monitor group underwent intra‐operative fluid management using an oesophageal Doppler‐guided stroke volume optimisation algorithm. Control group (conventional fluid therapy) intra‐operative fluid management was based on conventional haemodynamic indices. In a single centre, 102 patients were randomly assigned: 51 to the oesophageal Doppler monitor group (51 analysed) and 51 to the control group (50 analysed). Evaluators who were blinded to patient assignment collected postoperative outcome data. There was no difference in the length of postoperative hospital stay between the groups: median (IQR [range]) number of days until ready for discharge was 6 (5–8 [4–25]) days in the oesophageal Doppler monitor group compared with 7 (5–9 [4–42]) days in the control group, p = 0.5. There was no difference between the groups in postoperative morbidity survey scores on postoperative days 1, 3 or 5. Seven patients in the oesophageal Doppler monitor group and 11 in the control group experienced postoperative complications (p = 0.41). These findings question whether intra‐operative oesophageal Doppler‐guided fluid therapy is of benefit in patients undergoing open gynaecological surgery.
Heart Rate Variability and Procedural Outcome in Catheter Ablation for Atrial Fibrillation
Authors: Seaborn Geoffrey E.J. , Todd Keith , Michael Kevin A. , Baranchuk Adrian , Abdollah Hoshiar , Simpson Christopher S. , Akl Selim G. , Redfearn Damian P. 
Published: October 2013

IntroductionIn patients with normal hearts, increased vagal tone is associated with onset of paroxysmal atrial fibrillation (AF). Vagal denervation of the atria renders AF less inducible. Circumferential pulmonary vein isolation (CPVI) is effective for treating paroxysmal and persistent AF, and has been shown to impact heart rate variability (HRV) indices, in turn, reflecting vagal denervation. We examined the impact of CPVI on HRV indices, and evaluated the relationship between vagal modification and AF recurrence.MethodsElectrocardiogram recordings were collected from 83 consecutive patients (63 male, 20 female, age 56.9 ± 9.3 years) undergoing CPVI for paroxysmal (n = 56) or persistent (n = 27) AF. Recordings were obtained over 10 minutes preprocedure, and at intervals up to 12 months. Antiarrhythmic medications were suspended prior to CPVI, and were resumed for 3 months following. Success was defined as no recurrence of atrial arrhythmia lasting longer than 30 seconds.ResultsIn patients with successful procedures (n = 56, 42 paroxysmal, 14 persistent), HRV indices were significantly altered, with respect to preprocedure levels, over a sustained period. However, patients with recurrence (n = 27, 14 paroxysmal, 13 persistent) demonstrated similar HRV to their preprocedure levels over the follow‐up period.ConclusionOur results suggest that patients experiencing recurrence after a single CPVI have HRV attenuated by the procedure only intermittently, whereas patients with one successful CPVI experience a sustained change. A short‐term HRV recording is a convenient and potentially important marker for recurrence of atrial arrhythmia in a population undergoing CPVI.
Lomitapide at Supratherapeutic Plasma Levels Does Not Prolong the QTc Interval—Results from a TQT Study with Moxifloxacin and Ketoconazole
Authors: Darpo Borje , Ferber Georg , Zhou Meijian , Sumeray Mark , Sager Philip 
Published: October 2013

BackgroundThe aim of this study was to assess the effect of high plasma levels of lomitapide and its main metabolite on ECG parameters.MethodsIn this randomized five‐way cross‐over thorough QT study, 56 healthy subjects were enrolled. Study treatments were administered orally for 3 days in five separate periods in which subjects were dosed with (1) a single dose of 75 mg lomitapide on Day 1 followed by a single dose of 200 mg on Day 3; (2) ketoconazole 200 mg BID; (3) ketoconazole with a single dose of 75 mg lomitapide on Day 3; (4) a single dose of 400 mg moxifloxacin on Day 3 and (5) placebo.ResultsSingle doses of 75 and 200 mg lomitapide alone or in combination with ketoconazole caused minor changes in the change‐from‐baseline QTcI (ΔQTcI), whereas moxifloxacin and ketoconazole caused an increase of ΔQTcI with a peak effect at 1 and 3 hours postdosing, respectively. The largest mean placebo‐corrected ΔQTcI (ΔΔQTcI) for lomitapide did not exceed 3 ms (upper bound of 90% CI: 4.7 ms) at any time points postdosing. Ketoconazole caused mild QT prolongation with mean ΔΔQTcI of 5.9 and 6.5 ms at 2 and 3 hours postdosing, and exposure‐response analysis demonstrated a significantly positive slope of 1.3 ms per μg/mL (90% CI: 1.0–1.7). Moxifloxacin met the criteria for assay sensitivity.ConclusionsLomitapide does not have an effect on cardiac repolarization. The study's ability to detect small QTc changes was demonstrated with both moxifloxacin and ketoconazole.
Diagnostic Accuracy of a New Cardiac Electrical Biomarker for Detection of Electrocardiogram Changes Suggestive of Acute Myocardial Ischemic Injury
Authors: Schreck David M. , Fishberg Robert D. 
Published: October 2013

ObjectiveA new cardiac “electrical” biomarker (CEB) for detection of 12‐lead electrocardiogram (ECG) changes indicative of acute myocardial ischemic injury has been identified. Objective was to test CEB diagnostic accuracy.MethodsThis is a blinded, observational retrospective case‐control, noninferiority study. A total of 508 ECGs obtained from archived digital databases were interpreted by cardiologist and emergency physician (EP) blinded reference standards for presence of acute myocardial ischemic injury. CEB was constructed from three ECG cardiac monitoring leads using nonlinear modeling. Comparative active controls included ST voltage changes (J‐point, ST area under curve) and a computerized ECG interpretive algorithm (ECGI). Training set of 141 ECGs identified CEB cutoffs by receiver‐operating‐characteristic (ROC) analysis. Test set of 367 ECGs was analyzed for validation. Poor‐quality ECGs were excluded. Sensitivity, specificity, and negative and positive predictive values were calculated with 95% confidence intervals. Adjudication was performed by consensus.ResultsCEB demonstrated noninferiority to all active controls by hypothesis testing. CEB adjudication demonstrated 85.3–94.4% sensitivity, 92.5–93.0% specificity, 93.8–98.6% negative predictive value, and 74.6–83.5% positive predictive value. CEB was superior against all active controls in EP analysis, and against ST area under curve and ECGI by cardiologist.ConclusionCEB detects acute myocardial ischemic injury with high diagnostic accuracy. CEB is instantly constructed from three ECG leads on the cardiac monitor and displayed instantly allowing immediate cost‐effective identification of patients with acute ischemic injury during cardiac rhythm monitoring.