bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA metabarcoding reveals that 200‐μm‐size‐fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes
Authors: Liu Lemian , Liu Min , Wilkinson David M. , Chen Huihuang , Yu Xiaoqing , Yang Jun 
Published: January 2017

AbstractMicroeukaryotic plankton (0.2–200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High‐throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size‐fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore‐size sieve –by using SSU rDNA‐based high‐throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore‐size sieve. We further found that both >0.2 μm and 0.2–200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size‐fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.
Salvage high‐intensity focused ultrasound (HIFU) for locally recurrent prostate cancer after failed radiation therapy: Multi‐institutional analysis of 418 patients
Authors: Crouzet Sebastien , Blana Andreas , Murat Francois J. , Pasticier Gilles , Brown Stephen C. W. , Conti Giario N. , Ganzer Roman , Chapet Olivier , Gelet Albert , Chaussy Christian G. , Robertson Cary N. , Thuroff Stefan , Ward John F. 
Published: January 2017

ObjectiveTo report the oncological outcome of salvage high‐intensity focused ultrasound (S‐HIFU) for locally recurrent prostate cancer after external beam radiotherapy (EBRT) from a multicentre database.Patients and MethodsThis retrospective study comprises patients from nine centres with local recurrent disease after EBRT treated with S‐HIFU from 1995 to 2009. The biochemical failure‐free survival (bFFS) rate was based on the ‘Phoenix’ definition (PSA nadir + 2 ng/mL). Secondary endpoints included progression to metastasis and cancer‐specific death. Kaplan–Meier analysis was performed examining overall (OS), cancer‐specific (CSS) and metastasis‐free survival (MFS). Adverse events and quality of life status are reported.ResultsIn all, 418 patients with a mean (SD) follow‐up of 3.5 (2.5) years were included. The mean (SD) age was 68.6 (5.8) years and the PSA level before S‐HIFU was 6.8 (7.8) ng/mL. The median PSA nadir after S‐HIFU was 0.19 ng/mL. The OS, CSS and MFS rates at 7 years were 72%, 82% and 81%, respectively. At 5 years the bFFS rate was 58%, 51% and 36% for pre‐EBRT low‐, intermediate‐ and high‐risk patients, respectively. The 5‐year bFFS rate was 67%, 42% and 22% for pre‐S‐HIFU PSA level ≤4, 4–10 and ≥10 ng/mL, respectively. Complication rates decreased after the introduction of specific post‐RT parameters: incontinence (grade II or III) from 32% to 19% (P = 0.002); bladder outlet obstruction or stenosis from 30% to 15% (P = 0.003); recto‐urethral fistula decreased from 9% to 0.6% (P < 0.001). Study limitations include being a retrospective analysis from a registry with no control group.ConclusionS‐HIFU for locally recurrent prostate cancer after failed EBRT is associated with 7‐year CSS and MFS rates of >80% at a price of significant morbidity. S‐HIFU should be initiated early following EBRT failure
Novel approaches to the treatment of bacterial biofilm infections
Authors: Hughes Gareth , Webber Mark A 
Published: January 2017

Bacterial infection remains a major challenge to healthcare and is responsible for significant morbidity and mortality. This situation is becoming complicated by an increasingly ageing and susceptible population and large numbers of bacterial isolates, which have developed resistance to antibiotics. Bacteria that form biofilms and colonize or infect medical devices or wounds are particularly hard to treat as biofilms are inherently highly antibiotic resistant. Most infections have a component where bacteria exist as a biofilm and as a result, prevention or treatment of biofilm‐associated infections is highly important. A number of novel strategies to kill biofilms have been in development; these include the use of weak organic acids, photo irradiation and the application of bacteriophage. All have promise and are able to effectively kill biofilms in model systems, but for each there are still unanswered questions. This review summarizes the main features of biofilm infections, each of these novel approaches and the evidence that is still lacking before these potential treatments can be incorporated into clinical usage.Linked ArticlesThis article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro‐organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc
Immediate versus modified release hydrocortisone in mitotane‐treated patients with adrenocortical cancer
Authors: Weigel Marianne , Hahner Stefanie , Sherlock Mark , Agha Amar , Behan Lucy Ann , Stewart Paul M. , Arlt Wiebke , Beier Daniela , Frey Kathrin , Zopf Kathrin , Quinkler Marcus 
Published: January 2017

SummaryObjectiveMitotane induces hepatic CYP3A4 activity, resulting in accelerated cortisol inactivation, and also increases cortisol binding globulin (CBG). Therefore, higher hydrocortisone doses are required in patients with adrenocortical cancer (ACC) on mitotane treatment. Modified release hydrocortisone has not been used in mitotane‐treated ACC patients yet.AimCase series to compare serum cortisol, calculated free serum cortisol and ACTH levels in ACC patients on mitotane treatment with immediate and modified release hydrocortisone.DesignPharmacokinetics of immediate and modified release hydrocortisone, each administered at a dose of 40‐20‐0 mg, in nine patients with ACC and adjuvant mitotane treatment. For comparison, ten patients with secondary adrenal insufficiency (SAI) on three different hydrocortisone regimens and ten healthy males were included.MethodsSerum cortisol and plasma ACTH were measured by chemiluminescent enzyme immunoassay, and CBG by RIA, followed by calculation of free cortisol.ResultsCalculated free serum cortisol levels after 40 mg immediate release hydrocortisone in ACC patients (46 ± 14 nmol/l) were similar to those after 10 mg immediate release hydrocortisone intake in men with SAI (64 ± 16 nmol/l) or to the physiological morning free cortisol levels in healthy subjects (31 ± 5 nmol/l). Compared to immediate release hydrocortisone, free cortisol levels after 40 mg modified release hydrocortisone in ACC patients were significantly lower (12 ± 3 nmol/l; P = 0·03) resulting in a generally lower AUC (98 ± 21 vs 149 ± 37 nmol h/l; P = 0·02).Conclusions40‐20‐0 mg immediate release, but not modified release hydrocortisone, resulted in sufficient glucocorticoid coverage in patients with ACC receiving mitotane treatment. The use of equivalent doses of modified release hydrocortisone preparation should be avoided in patients on mitotane treatment.
Pharmacological indices and pulmonary distribution of rifampicin after repeated oral administration in healthy foals
Authors: Berlin S. , Kirschbaum A. , Spieckermann L. , Oswald S. , Keiser M. , Grube M. , Venner M. , Siegmund W. 
Published: January 2017

SummaryBackgroundThe treatment of equine lung infections by Rhodococcus equi with rifampicin is empirically based because pharmacokinetic/pharmacodynamic (PK/PD) indices and pivotal clinical outcome data are not available.ObjectivesTo evaluate the pharmacokinetics and pulmonary distribution of rifampicin into epithelial lining fluid (ELF) and bronchoalveolar lavage cells (BALC) to predict antimicrobial activity in the lung using PK/PD indices.Study designControlled, randomised, two‐period, crossover, repeated‐dose study with an initial arm to measure disposition after i.v. administration of rifampicin.MethodsPharmacokinetics and lung distribution were evaluated in six healthy foals treated with 10 mg/kg bwt rifampicin i.v. (initial arm) and with repeated oral doses of rifampicin at 10 mg/kg bwt and 20 mg/kg bwt once per day for 10 days (crossover arms). ELF and BALC were sampled by bronchoalveolar lavage 24 h after the last oral dosing. Rifampicin and 25‐O‐desacetyl rifampicin were quantified using liquid chromatography tandem‐mass spectrometry. Enzyme induction by rifampicin was confirmed by evaluation of plasma 4β‐OH‐cholesterol:cholesterol ratios.ResultsThe distribution volume of rifampicin administered i.v. was ~0.85 L/kg. Terminal elimination half‐life was ~11 h. Orally given rifampicin was slowly absorbed (Tmax, range: 2.5–8.0 h) and eliminated with apparent half‐lives of ~6–8 h. Trough concentrations in ELF and BALC were 1.01 ± 0.20 μg/mL and 1.25 ± 0.29 μg/mL, respectively, after 10 mg/kg bwt rifampicin and 2.71 ± 1.25 μg/mL and 3.09 ± 1.63 μg/mL, respectively, after 20 mg/kg bwt rifampicin. The average ratios of area under the plasma concentration time curve during an administration interval of 24 h (AUC0−24 h) to minimum inhibitory concentration (MIC) were 145 and 322 h, respectively, for less susceptible strains of R. equi (MIC90: 0.5 μg/mL).Main limitationsThe clearance and bioavailability of rifampicin after repeated oral dosing were not evaluated.ConclusionsTreatment with rifampicin at 10 mg/kg bwt administered once per day is suitable to generate drug concentrations above the MIC90 in the ELF and BALC of foals. Future clinical studies with rifampicin in combination with macrolide antibiotics with low drug interaction potential are required to translate the PK/PD indices into protocols for the treatment of R. equi lung infections.
Biologically agglutinated eukaryotic microfossil from Cryogenian cap carbonates
Authors: Moore K. R. , Bosak T. , Macdonald F. A. , Lahr D. J. G. , Newman S. , Settens C. , Pruss S. B. 
Published: January 2017

AbstractCryogenian cap carbonates that overlie Sturtian glacial deposits were formed during a post‐glacial transgression. Here, we describe microfossils from the Kakontwe Formation of Zambia and the Taishir Formation of Mongolia—both Cryogenian age, post‐Sturtian cap carbonates—and investigate processes involved in their formation and preservation. We compare microfossils from these two localities to an assemblage of well‐documented microfossils previously described in the post‐Sturtian Rasthof Formation of Namibia. Microfossils from both new localities have 10 ± 1 μm‐thick walls composed of carbonaceous matter and aluminosilicate minerals. Those found in the Kakontwe Formation are spherical or ovoid and 90 ± 5 μm to 200 ± 5 μm wide. Structures found in the Taishir Formation are mostly spherical, 50 ± 5 μm to 140 ± 5 μm wide, with distinct features such as blunt or concave edges. Chemical and mineralogical analyses show that the walled structures and the clay fraction extracted from the surrounding sediments are composed of clay minerals, especially muscovite and illite, as well as quartz, iron and titanium oxides, and some dolomite and feldspar. At each locality, the mineralogy of the microfossil walls matched that of the clay fractions of the surrounding sediment. The abundance of these minerals in the walled microfossils relative to the surrounding carbonate matrix and microbial laminae, and the presence of minerals that cannot precipitate from solution (titanium oxide and feldspar), suggests that the composition represents the original mineralogy of the structures. Furthermore, the consistency in mineralogy of both microfossils and sediments across the three basins, and the uniformity of size and shape among mineral grains in the fossil walls indicate that these organisms incorporated these minerals by primary biological agglutination. The discovery of new, mineral‐rich microfossil assemblages in microbially laminated and other fine‐grained facies of Cryogenian cap carbonates from multiple localities on different palaeocontinents demonstrates that agglutinating eukaryotes were widespread in carbonate‐dominated marine environments in the aftermath of the Sturtian glaciation.
Landscape genetics indicate recently increased habitat fragmentation in African forest‐associated chafers
Authors: Eberle Jonas , Rödder Dennis , Beckett Marc , Ahrens Dirk 
Published: January 2017

AbstractToday, indigenous forests cover less than 0.6% of South Africa's land surface and are highly fragmented. Most forest relicts are very small and typically occur in fire‐protected gorges along the eastern Great Escarpment. Yet, they hold a unique and valuable fauna with high endemism and ancient phylogenetic lineages, fostered by long‐term climatic stability and complex microclimates. Despite numerous studies on southern African vegetation cover, the current state of knowledge about the natural extension of indigenous forests is rather fragmentary. We use an integrated approach of population‐level phylogeography and climatic niche modeling of forest‐associated chafer species to assess connectivity and extent of forest habitats since the last glacial maximum. Current and past species distribution models ascertained potential fluctuations of forest distribution and supported a much wider potential current extension of forests based on climatic data. Considerable genetic admixture of mitochondrial and nuclearDNAamong many populations and an increase in mean population mutation rate in Extended Bayesian Skyline Plots of all species indicated more extended or better connected forests in the recent past (<5 kya). Genetic isolation of certain populations, as revealed by population differentiation statistics (), as well as landscape connectivity statistics and habitat succession scenarios suggests considerable loss of habitat connectivity. As major anthropogenic influence is likely, conservational actions need to be considered.
The combined and separate impacts of climate extremes on the current and future US rainfed maize and soybean production under elevated CO2
Authors: Jin Zhenong , Zhuang Qianlai , Wang Jiali , Archontoulis Sotirios V. , Zobel Zachary , Kotamarthi Veerabhadra R. 
Published: January 2017

AbstractHeat and drought are two emerging climatic threats to the US maize and soybean production, yet their impacts on yields are collectively determined by the magnitude of climate change and rising atmospheric CO2 concentrations. This study quantifies the combined and separate impacts of high temperature, heat and drought stresses on the current and future US rainfed maize and soybean production and for the first time characterizes spatial shifts in the relative importance of individual stress. Crop yields are simulated using the Agricultural Production Systems Simulator (APSIM), driven by high‐resolution (12 km) dynamically downscaled climate projections for 1995–2004 and 2085–2094. Results show that maize and soybean yield losses are prominent in the US Midwest by the late 21st century under both Representative Concentration Pathway (RCP) 4.5 and RCP8.5 scenarios, and the magnitude of loss highly depends on the current vulnerability and changes in climate extremes. Elevated atmospheric CO2 partially but not completely offsets the yield gaps caused by climate extremes, and the effect is greater in soybean than in maize. Our simulations suggest that drought will continue to be the largest threat to US rainfed maize production under RCP4.5 and soybean production under both RCP scenarios, whereas high temperature and heat stress take over the dominant stress of drought on maize under RCP8.5. We also reveal that shifts in the geographic distributions of dominant stresses are characterized by the increase in concurrent stresses, especially for the US Midwest. These findings imply the importance of considering heat and drought stresses simultaneously for future agronomic adaptation and mitigation strategies, particularly for breeding programs and crop management. The modeling framework of partitioning the total effects of climate change into individual stress impacts can be applied to the study of other crops and agriculture systems.
Pathogenetic determinants in Kawasaki disease: the haematological point of view
Authors: Del Principe Domenico , Pietraforte Donatella , Gambardella Lucrezia , Marchesi Alessandra , Tarissi de Jacobis Isabella , Villani Alberto , Malorni Walter , Straface Elisabetta 
Published: January 2017

AbstractKawasaki disease is a multisystemic vasculitis that can result in coronary artery lesions. It predominantly affects young children and is characterized by prolonged fever, diffuse mucosal inflammation, indurative oedema of the hands and feet, a polymorphous skin rash and non‐suppurative lymphadenopathy. Coronary artery involvement is the most important complication of Kawasaki disease and may cause significant coronary stenosis resulting in ischemic heart disease. The introduction of intravenous immunoglobulin decreases the incidence of coronary artery lesions to less than 5%. The etiopathogenesis of this disease remains unclear. Several lines of evidence suggest that an interplay between a microbial infection and a genetic predisposition could take place in the development of the disease. In this review, we summarize the state of the art of pathogenetic mechanisms of Kawasaki disease underscoring the relevance of haematological features as a novel field of investigation.
Volumetric assessment of alveolar clefts: a literature review
Authors: Blessmann Weber João Batista , de Macedo Menezes Luciane , Azeredo Fabiane , Lessa Filho Luciano Schwartz 
Published: January 2017

ObjectiveTo conduct a review of the literature on methods for volumetric assessment of alveolar clefts and ascertain which methods are most precise to guide future research.MethodsThe PubMed and MEDLINE databases were searched for English‐language reports of clinical and in vitro studies with detailed descriptions of imaging modality, sample characteristics, and method for measurement of alveolar cleft volume.ResultsThe search strategy yielded 34 articles, of which 14 were selected for in‐depth analysis. According to the findings of computed tomography (CT)‐based studies, the CT modalities and software employed for assessment were deemed reliable and satisfactory.ConclusionsMeasurement of alveolar cleft volume by the proposed methods and using the equipment and software employed in the analyzed studies has high efficacy and efficiency and can be safely used for cleft lip and palate treatment planning.
Effects of different sources of protein on the growth performance, blood chemistry and polypeptide profiles in the gastrointestinal tract digesta of newly weaned piglets
Authors: Zhong R. Z. , Xia J. Q. , Sun H. , Qin G. X. 
Published: January 2017

SummaryTo determine the effects of different sources of protein on the growth performance of newly weaned piglets, 72 newly weaned piglets were randomly assigned to three groups fed different diets (soya bean, casein and dried distillers' grain with solubles (DDGS) feeds). Casein and DDGS feeds consisted of soya bean feed in which 5% of the CP was replaced with casein‐ or DDGS‐derived CP respectively. Blood and chyme samples were collected from each piglet 2 h post‐feeding on days 0 and 28 of the feeding period. The DDGS feed decreased DMI (p = 0.024) and increased FCR (p = 0.025) due to lower nitrogen utilization (p = 0.078) than those of other feeds. Total amino acid content in chyme demonstrated that casein feed digested rapidly in the duodenum (p = 0.005), whereas DDGS feed was digested primarily in the distal jejunum (p = 0.003) and ileocecum (p = 0.002). However, polypeptide profiles in chyme exhibited a pattern different from those of amino acids. There were no differences in the polypeptide profiles in the stomachs of piglets fed soya bean or casein feeds (p > 0.05), but soya bean group had greater amounts of small polypeptides (mass under m/z 3000 Da) in the duodenum (p = 0.052) than other groups. In contrast, the DDGS feed group had more large polypeptides (m/z 3000–4000 Da) in the stomach than the other groups (p < 0.001). In addition, 10 pairs of polypeptides with matching masses were identified in the plasma and digesta, indicating that polypeptides may have been transported across the intestinal epithelial cells and into the blood. Taken together, substitution of 5% of the CP in soya bean meal‐based feed with DDGS‐derived CP decreased the growth performance of newly weaned piglets due to poor digestibility and N utilization of DDGS feed, as well as untimely digestion of casein feed.
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers
Authors: Zhong Xiaoxiao , Li Qi , Kong Lingfeng , Yu Hong 
Published: January 2017

AbstractThe level and extent of linkage disequilibrium (LD) and effective population size (Ne) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas, using 61 single‐nucleotide polymorphisms. Significant differences were detected in the average r2 between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population‐specific critical values (P<0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0–0.23 cM) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker‐assisted selection in oysters.