bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross‐specific and species‐specific amplifications
Authors: Queirós J. , Godinho R. , Lopes S. , Gortazar C. , de la Fuente J. , Alves P. C. 
Published: November 2014

AbstractAlthough whole‐genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross‐specific and species‐specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species‐specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity‐fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.
In situ expression of nitrite‐dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co‐occurring with expressed anammox proteins in a contaminated aquifer
Authors: Hanson Buck T. , Madsen Eugene L. 
Published: November 2014

SummaryDeciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar‐contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS‐PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragment analysis using nano‐liquid chromatography (LC)‐mass spectrometry (MS)/MS of the three protein pools generated a total of 95 725 mass spectra. When analyzed using mascot v.2.3.02 and searched against the NCBInr bacterial database [confidence interval 99% (P < 0.01)], a total of 1 270 proteins had at least two peptide matches. Replication of identified proteins across the three libraries was low (3.3%); however, in each library, the most frequently identified protein host was Candidatus Methylomirabilis oxyfera (15, 12 and 62 proteins for each shotgun and the gel‐slice library respectively). Remarkably, eight of the nine proteins in the nitrite‐dependent anaerobic methane oxidation pathway were found. Additionally, 39 proteins were matched to known anammox bacteria including hydroxylamine and hydrazine oxidase. Metaproteomics thus revealed a microbial population, closely related to Ca. Methylomirabilis oxyfera, actively engaged in nitrite‐dependent anaerobic methane oxidation and likely competing for nitrite with anammox bacteria.
Dissolved organic monomer partitioning among bacterial groups in two oligotrophic lakes
Authors: Pérez María Teresa , Rofner Carina , Sommaruga Ruben 
Published: November 2014

SummaryUnderstanding how resource partitioning works among taxa is crucial in explaining coexistence and competition within a community. Here, we assessed resource partitioning among freshwater bacterial groups from two oligotrophic lakes using four types of organic substrates as compound models. Substrate uptake patterns were examined by microautoradiography combined with catalysed reporter deposition fluorescent in situ hybridization. Four large taxonomic groups were found in the lakes, but Actinobacteria (AcI lineage) and Betaproteobacteria (R‐BTcluster) dominated the bacterial assemblage. Monomers containing nitrogen and/or phosphorus were preferred over the ones containing only carbon. All groups were able to incorporate amino acids, adenosine triphosphate and glucose. However, acetate was only taken up by ∼ 10–12% of bacteria, and its uptake was not detected in Cytophaga‐Flavobacteria. Apart from acetate, the contribution of a particular bacterial group to the uptake of a substrate was proportional to its relative abundance. In both lakes, we detected substrate partitioning between AcI Actinobacteria, which was overrepresented in glucose and acetate utilization, and R‐BT Betaproteobacteria, which dominated amino acid uptake. Our results strongly point to physiological niche separation of those bacterial groups in alpine lakes.
Draft whole‐genome sequence of the antibiotic‐producing soil isolate Pseudomonas sp. strain 250J
Authors: Molina‐Santiago Carlos , Udaondo Zulema , Ramos Juan‐Luis 
Published: November 2014

SummaryBacteria of the genus Pseudomonas are becoming increasing well known for their ability to produce a wide range of antimicrobial compounds. In a large‐scale screening for antibiotic producers, we identified a soil isolate that uses 4‐hydroxyphenylacetate as the sole carbon source, Pseudomonas sp. strain 250J, which produces cyclic lipodepsipeptides of the xantholysin family during the stationary phase of growth. The closest relatives of this strain are Pseudomonas mosselii, Pseudomonas soli and Pseudomonas entomophila. Sequencing of the 250J genome allowed us to find the genes relevant to antibiotic production, those which allow utilization of 4‐hydroxyphenylacetate as a sole carbon source and a set of genes potentially involved in biocontrol.
Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet
Authors: Stibal Marek , Schostag Morten , Cameron Karen A. , Hansen Lars H. , Chandler David M. , Wadham Jemma L. , Jacobsen Carsten S. 
Published: November 2014

SummaryBiological processes in the supraglacial ecosystem, including cryoconite, contribute to nutrient cycling within the cryosphere and may affect surface melting, yet little is known of the diversity of the active microbes in these environments. We examined the bacterial abundance and community composition of cryoconite over a melt season at two contrasting sites at the margin and in the interior of the Greenland ice sheet, using sequence analysis and quantitative polymerase chain reaction of coextracted 16S rDNA and rRNA. Significant differences were found between bulk (rDNA) and potentially active (rRNA) communities, and between communities sampled from the two sites. Higher concentrations of rRNA than rDNA were detected at the interior site, whereas at the margin several orders of magnitude less rRNA was found compared with rDNA, which may be explained by a lower proportion of active bacteria at the margin site. The rRNA communities at both sites were dominated by a few taxa of Cyanobacteria and Alpha‐ and/or Betaproteobacteria. The bulk alpha diversity was higher in the margin site community, suggesting that local sources may be contributing towards the gene pool in addition to long distance transport.
Immunoreactivity of the 14F7 Mab raised against N‐Glycolyl GM3 Ganglioside in retinoblastoma tumours
Authors: Torbidoni Ana Vanesa , Scursoni Alejandra , Camarero Sandra , Segatori Valeria , Gabri Mariano , Alonso Daniel , Chantada Guillermo , de Dávila María Teresa G. 
Published: November 2014

AbstractIntroductionThe identification of molecules expressed selectively on the surface of retinoblastoma cells would allow applying targeted therapies. The Ganglioside, N‐Glycolyl‐GM3 (NeuGc‐GM3), is an attractive candidate, as it has been detected in other paediatric neuroectodermic tumours, and it is not expressed in human normal tissues. The 14F7 antibody recognizes specifically the ganglioside NeuGc‐GM3.PurposeTo characterize the expression of NeuGc‐GM3 in retinoblastoma cell lines and in retinoblastoma tumours using the 14F7 monoclonal antibody.MethodsWe studied WERI‐Rb1 and Y79 cell lines, 24 retinoblastoma primary tumours from unilateral and bilateral cases and two bone marrow biopsies from metastatic retinoblastoma. Tumours were classified into three groups: non‐invasive (n = 13), invasive (n = 9) and metastatic (n = 2). Three eyes enucleated because of non‐tumoural conditions were used as controls. Cell lines and tumour sections were studied by immunohistochemistry using the 14F7 antibody. NeuGc‐GM3 expression was evaluated by analysing the percentage of positive tumoural cells and the staining intensity. These parameters were analysed comparatively among the three groups.ResultsBoth retinoblastoma cell lines showed immunoreactivity to NeuGc‐GM3 but WERI‐Rb1 presented higher intensity than Y79. All the tumours studied showed strong immunoreactivity to NeuGc‐GM3 with no significant differences among groups. In both bone marrow specimens, NeuGc‐GM3 immunoreactivity was observed in retinoblastoma cells. In bilaterally enucleated cases, NeuGc‐GM3 immunoreactivity was not altered before and after chemotherapy. Non‐tumoural retinas were negative.ConclusionsNeuGc‐GM3 is highly expressed in retinoblastoma cell lines, tumours and metastatic cells to the bone marrow, and it is not detectable in control eyes. There were no significant differences in the immunoreactivity to 14F7 among tumours from different disease stages. Its immunoreactivity did not change after chemotherapy.
Pharmacokinetic–pharmacodynamic modelling of intravenous and oral topiramate and its effect on phonemic fluency in adult healthy volunteers
Authors: Ahmed Ghada F. , Marino Susan E. , Brundage Richard C. , Pakhomov Serguei V. S. , Leppik Ilo E. , Cloyd James C. , Clark Annie , Birnbaum Angela K. 
Published: November 2014

AimsThe aim was to develop a quantitative approach that characterizes the magnitude of and variability in phonemic generative fluency scores as measured by the Controlled Oral Word Association (COWA) test in healthy volunteers after administration of an oral and a novel intravenous (IV) formulation of topiramate (TPM).MethodsNonlinear mixed‐effects modelling was used to describe the plasma TPM concentrations resulting from oral or IV administration. A pharmacokinetic–pharmacodynamic (PK‐PD) model was developed sequentially to characterize the effect of TPM concentrations on COWA with different distributional assumptions.ResultsTopiramate was rapidly absorbed, with a median time to maximal concentration of 1 h and an oral bioavailability of ∼100%. Baseline COWA score increased by an average of 12% after the third administration on drug‐free sessions. An exponential model described the decline of COWA scores, which decreased by 14.5% for each 1 mg l−1 increase in TPM concentration. The COWA scores were described equally well by both continuous normal and Poisson distributions.ConclusionsThis analysis quantified the effect of TPM exposure on generative verbal fluency as measured by COWA. Repetitive administration of COWA resulted in a better performance, possibly due to a learning effect. The model predicts a 27% reduction in the COWA score at the average observed maximal plasma concentration after a 100 mg dose of TPM. The single‐dose administration of relatively low TPM doses and narrow range of resultant concentrations in our study were limitations to investigating the PK‐PD relationship at higher TPM exposures. Hence, the findings may not be readily generalized to the broader patient population.
A Phase II trial of Belinostat (PXD101) in patients with relapsed or refractory peripheral or cutaneous T‐cell lymphoma
Authors: Foss Francine , Advani Ranjana , Duvic Madeleine , Hymes Kenneth B. , Intragumtornchai Tanin , Lekhakula Arnuparp , Shpilberg Ofer , Lerner Adam , Belt Robert J. , Jacobsen Eric D. , Laurent Guy , Ben‐Yehuda Dina , Beylot‐Barry Marie , Hillen Uwe , Knoblauch Poul , Bhat Gajanan , Chawla Shanta , Allen Lee F. , Pohlman Brad 
Published: November 2014

SummaryBelinostat is a pan‐histone deacetylase inhibitor with antitumour and anti‐angiogenic properties. An open label, multicentre study was conducted in patients with peripheral T‐cell lymphoma (PTCL) or cutaneous T‐cell lymphoma (CTCL) who failed ≥1 prior systemic therapy and were treated with belinostat (1000 mg/m2 intravenously ×5 d of a 21‐d cycle). The primary endpoint was objective response rate (ORR). Patients with PTCL (n = 24) had received a median of three prior systemic therapies (range 1–9) and 40% had stage IV disease. Patients with CTCL (n = 29) had received a median of one prior skin‐directed therapy (range 0–4) and four prior systemic therapies (range 1–9); 55% had stage IV disease. The ORRs were 25% (PTCL) and 14% (CTCL). Treatment‐related adverse events occurred in 77% of patients; nausea (43%), vomiting (21%), infusion site pain (13%) and dizziness (11%) had the highest incidence. Treatment‐related serious adverse events were Grade 5 ventricular fibrillation; Grade 4 thrombocytopenia; Grade 3 peripheral oedema, apraxia, paralytic ileus and pneumonitis; and Grade 2 jugular vein thrombosis. Belinostat monotherapy was well tolerated and efficacious in patients with recurrent/refractory PTCL and CTCL. This trial was registered at www.clinicaltrials.gov as NCT00274651.
A Critical Evaluation of the Gamma‐Hydroxybutyrate (GHB) Model of Absence Seizures
Authors: Venzi Marcello , Di Giovanni Giuseppe , Crunelli Vincenzo 
Published: November 2014

SummaryTypical absence seizures (ASs) are nonconvulsive epileptic events which are commonly observed in pediatric and juvenile epilepsies and may be present in adults suffering from other idiopathic generalized epilepsies. Our understanding of the pathophysiological mechanisms of ASs has been greatly advanced by the availability of genetic and pharmacological models, in particular the γ‐hydroxybutyrate (GHB) model which, in recent years, has been extensively used in studies in transgenic mice. GHB is an endogenous brain molecule that upon administration to various species, including humans, induces not only ASs but also a state of sedation/hypnosis. Analysis of the available data clearly indicates that only in the rat does there exist a set of GHB‐elicited behavioral and EEG events that can be confidently classified as ASs. Other GHB activities, particularly in mice, appear to be mostly of a sedative/hypnotic nature: thus, their relevance to ASs requires further investigation. At the molecular level, GHB acts as a weak GABA‐B agonist, while the existence of a GHB receptor remains elusive. The pre‐ and postsynaptic actions underlying GHB‐elicited ASs have been thoroughly elucidated in thalamus, but little is known about the cellular/network effects of GHB in neocortex, the other brain region involved in the generation of ASs.
Effect of Sex and Age Interactions on Functional Outcome after Stroke
Authors: Kim Tae‐Hee , Vemuganti Raghu 
Published: November 2014

SummaryStroke is one of the leading causes of death and disability worldwide. Experimental and clinical studies showed that sex and age play an important role in deciding the outcome after stroke. At younger ages, males were shown to have a higher risk for stroke than females. However, this trend reverses in older ages particularly when females reach menopause. Many preclinical studies indicate that steroid hormones modulate the age‐dependent differential stroke outcome. In addition, patterns of cell death pathways activated following cerebral ischemia are distinct between males and females, but independent of steroid hormones. Recent studies also indicate that microRNAs play important roles in mediating sex‐specific stroke outcome by regulating stroke‐related genes. This review discusses the contribution of sex and age to outcome after stroke with particular emphasis on the experimental studies that examined the effects of steroid hormones, differential cell death pathways, and involvement of sex‐specific microRNAs following cerebral ischemia. Current understanding of the role of thrombolytic agents in stroke therapy is also discussed.
Safety and efficacy of pre‐incisional peritonsillar lornoxicam in paediatric post‐tonsillectomy pain: a prospective double‐blind, placebo‐controlled, split‐body clinical study
Authors: Abdel‐Ghaffar H.S. , Abdel‐Azeem H.G. , Roushdy M.M. 
Published: November 2014

ObjectivesTo evaluate the risk of peri‐operative bleeding and re‐intervention with peritonsillar lornoxicam infiltration in paediatric tonsillectomy.DesignProspective, randomised, double‐blinded, placebo‐controlled, split‐body study.SettingUniversity hospital.ParticipantsA total of 68 patients (7–15 years), ASA I–II, scheduled for tonsillectomy divided into two groups (n = 34) to receive bilateral peritonsillar saline infiltration (placebo group) or peritonsillar saline infiltration in one tonsil (placebo side) and 8 mg lornoxicam in the other tonsil (intervention side; study group). Drugs were administered after induction of anaesthesia and before start of surgery.Main outcome measuresIntra‐operative and postoperative bleeding score, platelet aggregometry before and 30 min after study drug administration, the verbal rating pain scale, time to first postoperative analgesic request, total analgesic consumption during 1st 24 h postoperative and adverse effects were evaluated.ResultsThe difference in bleeding score between groups did not reach our definition of statistical significance (P < 0.05). Platelet aggregometry tests did not change significantly with time between groups. Lower postoperative pain scores, longer time to first analgesic request (372.76 ± 82.15 versus 64.89 ± 25.76 min P < 0.001) and lower paracetamol consumption (421.76 ± 125.63 versus 690.29 ± 141.47 mg, P < 0.001) were recorded in study group compared with control group. No patient required hospital re‐admission or re‐operation because of postoperative tonsillar bed bleeding.ConclusionsThe lack of significant complications suggests that pre‐incisional peritonsillar lornoxicam followed by intravenous paracetamol rescue analgesia may be safe for tonsillectomy in children. To avoid conflict with intra‐operative bleeding, postoperative infiltration of lornoxicam is recommended.
Effect of fragmentation on predation pressure of insect herbivores in a north temperate deciduous forest ecosystem
Authors: MAGUIRE DOROTHY Y. , NICOLE THOMAS , BUDDLE CHRISTOPHER M. , BENNETT ELENA M. 
Published: November 2014

1. Forest fragmentation affects many ecosystem processes by spatially altering relationships among organisms. Herbivory by arthropods is an important ecosystem processes in forests that fragmentation alters by changing relationships among herbivores, their predators, and their hosts. The relative importance of these factors remains unclear.2. It was tested whether the exclusion of vertebrate predators affected the arthropod abundance or amounts of herbivory in a fragmented, deciduous forest landscape in southern Quebec. Differences in the abundance of arthropod herbivores and amounts of herbivory in forest patches with different landscape characteristics (small isolated patches versus large connected ones), on sugar maple saplings with or without exclosures that restricted access by large vertebrate predators were measured.3. Saplings protected from predators with exclosures had greater abundances of all arthropods (herbivores and invertebrate predators) than those without, indicating potential top‐down effects of vertebrate predators on arthropods. Analysis of effect sizes between exclosure treatments and controls suggests the magnitude of predation effects may be affected by fragmentation.4. Strong top‐down effects of predators on arthropods, and weak effects of fragmentation on predation or amounts of herbivory were found. As a result, herbivory may be regulated by factors other than vertebrate predation in this system.
Effects of soil nutrients on the sequestration of plant defence chemicals by the specialist insect herbivore, Danaus plexippus
Authors: TAO LEILING , HUNTER MARK D. 
Published: November 2014

1. Although anthropogenic nitrogen (N) enrichment has significantly changed the growth, survival and reproduction of herbivorous insects, its effects on the defensive sequestration of secondary chemicals by insect herbivores are less well understood. Previous studies have shown that soil nutrient availability can affect sequestration directly through changing concentrations of plant defence chemicals, or indirectly through altering growth rates of herbivores. There has been less exploration of how nutrient deposition affects the consumption of secondary chemicals and subsequent sequestration efficiency. In the current study, the overall effect of soil N availability on cardenolide sequestration by the monarch caterpillar Danaus plexippus was examined. Specifically, the effects of soil nutrient availability on growth, consumption, excretion and sequestration efficiency of cardenolides by D. plexippus larvae fed on the tropical milkweed Asclepias curassavica were measured.2. The results showed that soil N and phosphorus (P) fertilisation significantly reduced caterpillar growth rate and the sequestration efficiency of cardenolides by monarch caterpillars feeding on A. curassavica. The lowered sequestration efficiency was accompanied by higher concentrations of cardenolides in frass. Although the total cardenolide contents of caterpillars were lower under high N or P fertilisation levels, caterpillar cardenolide concentrations were constant across fertilisation treatments because of lower growth rates (and therefore lower body mass) under high fertilisation. It is concluded that anthropogenic N deposition may have multiple effects on insect herbivores, including their ability to defend themselves from predators with sequestered plant defences.