bluuebunny/crossref_metadata_2025_split huggingface dataset:
A harvest of weeds yields insight into a case of contemporary evolution
Authors: Franks Steven J. 
Published: September 2016

When Charles Darwin was exploring the idea of evolution via natural selection, he looked to domesticated species, with the opening chapter of The Origin of Species titled ‘Variation Under Domestication’ (Darwin ). Domesticated species such as crops are a great example of artificial selection, which Darwin realized was analogous to natural selection. But growing among those carefully selected crop varieties are the unwelcome and unwanted plants we call weeds. Despite the importance of weeds and long‐standing interest in their evolution (Baker ), we still know little about how agricultural weeds evolve, and we often fail to take evolution into account when attempting to manage them (Neve et al. ). Agricultural weeds are subjected to the unique conditions of farm fields, such as frequent soil disturbance and the addition of water and nutrients. They are also confronted with aggressive attempts at their removal via herbicides and mechanical means. As such, they are under intense demographic and selective pressure and can potentially rapidly evolve in response. In this issue of Molecular Ecology, Kuester and co‐authors make a rare attempt to understand contemporary evolution in an agricultural weed (Kuester et al. ). They do so using the powerful resurrection approach of comparing ancestors and descendants under common conditions (Franks et al. ). They sampled multiple populations of the weedy plant Ipomoea purpurea at two points in time. A comparison of these greenhouse‐grown ancestor and descendent populations showed that, over time, populations had lost significant levels of neutral genetic diversity, consistent with genetic bottlenecks. The authors also found a slight increase, on average, of resistance to the herbicide glyphosate, which is the active ingredient in Roundup®. This work is one of a growing number of studies demonstrating rapid evolution in natural populations (Thompson ) and also reveals evidence of both selection and drift in populations of an agricultural weed.
Molecular identification, antifungal resistance and virulence of Cryptococcus neoformans and Cryptococcus deneoformans isolated in Seville, Spain
Authors: Gago Sara , Serrano Carmen , Alastruey‐Izquierdo Ana , Cuesta Isabel , Martín‐Mazuelos Estrella , Aller Ana Isabel , Gómez‐López Alicia , Mellado Emilia 
Published: September 2016

SummaryCryptococcal meningitis is one of the leading causes of death in HIV/AIDS patients. Our aim was to in order to characterise the epidemiology, antifungal susceptibility pattern and virulence of 28 Cyptococcus sp. strains recovered from 12 AIDS patients during two years in a Spanish single institution. Antifungal susceptibility testing was performed according to the CLSI protocols. Clinical strains were molecularly characterised by serotyping, mating type, PCR fingerprinting (M13 and GACA4 microsatellites) and analysis of two rDNA regions (IGS1 and ITS). Sequencing of the ERG11 gene was used to explore mechanisms of fluconazole resistance. Differences in virulence between species were studied in a Galleria mellonella infection model. Cryptococcus deneoformans and C. deneoformans x Cryptococcus neoformans hybrids were the most frequent variety (65%) followed by C. neoformans (35%). Strains were categorised according to 13 microsatellite genotypes and mixed infections could be detected in three patients. Twenty‐nine per cent of the strains were fluconazole resistant. In one of the patients, the fluconazole resistance phenotype was associated with a point mutation in the ERG11 gene responsible for the amino acid substitution G470R. C. neoformans strains were able to kill G. mellonella larvae more efficiently than C. deneoformans and hybrids between both species. Precisely molecular characterisation of C. neoformans species is important for an accurate patient's management.
Environmental preferences of brachiopods and bivalves across major climatic changes during the Late Palaeozoic ice age (Pennsylvanian, western Argentina)
Authors: Balseiro Diego , Halpern Karen 
Published: September 2016

AbstractDuring the late Palaeozoic ice age (LPIA), ice‐proximal marine regional communities record contrasting responses to climate change compared to ice‐distal communities. However, there is still much to be understood in distal regions in order to fully understand the palaeobiological consequences of the LPIA. Here, were analyse brachiopod and bivalve environmental preferences along the bathymetric gradient during a major glacial event and the subsequent non‐glacial interval in western Argentina. Median environmental breadths did not change with the reassembly of communities during the non‐glacial interval. Moreover, bivalves and brachiopod immigrants show similar environmental breadths although they tend to have immigrated from different palaeogeographical regions. These patterns reinforce the idea that the worldwide marine fauna was probably culled of stenotopic taxa during the LPIA. On the other hand, analysis of the preferred depths of survivors and immigrants sheds light on the substantial modification of the bathymetric diversity gradient. Among different possible explanations, the immigration of taxa with affinities for deep environments is the only one supported. In addition, results underscore the observation that the higher turnover in the offshore environment was probably driven by immigration rather than extinction. Finally, stability in environmental preferences at a regional scale is not mirrored by stability in survivors’ individual preferences, because survivors’ preferred depth is not correlated during the glacial and non‐glacial intervals. Moreover, the amount of change in survivors preferred depth is not related to their environmental breadth, nor to their occupancy. These patterns suggest: (1) instability in realized niches; and (2) individual responses of survivor genera.
Systematic and palaeoecological significance of the first record of Pygocephalomorpha females bearing oöstegites (Malacostraca, Peracarida) from the lower Permian of southern Brazil
Authors: Pazinato Paula Giovana , Soares Marina Bento , Adami‐Rodrigues Karen 
Published: September 2016

AbstractMalacostracan crustaceans of the fossil order Pygocephalomorpha are conspicuous elements in brackish to freshwater faunas in the upper Carboniferous of Laurentia and lower Permian of Gondwana. A pronounced sexual dimorphism is recognizable within its members, with Pygocephalomorpha females bearing oöstegites: modified epipodites that hold a brood pouch where the eggs develop until juvenile stage, with no planktonic dispersal of larvae. The preservation of oöstegites is quite rare and is described here for the first time from the American continents. The specimens, ventrally preservedLiocaris hueneifemales bearing oöstegites, come from the Irati Formation, a lower Permian sequence of the Paraná Basin, from an outcrop in southern Brazil. The oöstegites are similar to those previously described for Pygocephalomorpha, displaying seven pairs of overlapping epipodites that cover the whole cephalothorax. The scarcity of these structures in the fossil record may be explained by taphonomic bias (it requires ventrally preserved crustaceans) but more likely by palaeobiological aspects, such as preservation of an ovigerous moult. The record from the Irati Formation suggests that pygocephalomorphs had seasonal reproduction, with females maturing at the same time and acquiring oöstegites that would be lost after the release of juveniles. This record confirms the relationship of the BrazilianLiocarisBeurlen to the EnglishPygocephalusHuxley and South AfricanNotocarisBroom pygocephalomorphs and provides an insight into its palaeoecological significance.
Barley HvPAPhy_a as transgene provides high and stable phytase activities in mature barley straw and in grains
Authors: Holme Inger Bæksted , Dionisio Giuseppe , Madsen Claus Krogh , Brinch‐Pedersen Henrik 
Published: September 2016

SummaryThe phytase purple acid phosphatase (HvPAPhy_a) expressed during barley seed development was evaluated as transgene for overexpression in barley. The phytase was expressed constitutively driven by the cauliflower mosaic virus 35S‐promoter, and the phytase activity was measured in the mature grains, the green leaves and in the dry mature vegetative plant parts left after harvest of the grains. The T2‐generation of HvPAPhy_a transformed barley showed phytase activity increases up to 19‐fold (29 000 phytase units (FTU) per kg in mature grains). Moreover, also in green leaves and mature dry straw, phytase activities were increased significantly by 110‐fold (52 000 FTU/kg) and 57‐fold (51 000 FTU/kg), respectively. The HvPAPhy_a‐transformed barley plants with high phytase activities possess triple potential utilities for the improvement of phosphate bioavailability. First of all, the utilization of the mature grains as feed to increase the release of bio‐available phosphate and minerals bound to the phytate of the grains; secondly, the utilization of the powdered straw either directly or phytase extracted hereof as a supplement to high phytate feed or food; and finally, the use of the stubble to be ploughed into the soil for mobilizing phytate‐bound phosphate for plant growth.
Screening of carnitine and biotin deficiencies on tandem mass spectrometry
Authors: Hagiwara Shin‐ichiro , Kubota Mitsuru , Nambu Ryusuke , Kagimoto Seiichi 
Published: September 2016

AbstractBackgroundIt is important to assess pediatric patients for nutritional deficiency when they are receiving specific interventions, such as enteral feeding. We focused on measurement of C0 and 3‐hydroxyisovalerylcarnitine (C5‐OH) with tandem mass spectrometry (MS/MS), which is performed as part of the newborn mass screening. The purpose of this study was to investigate the usefulness of MS/MS for screening carnitine and biotin deficiencies.MethodsForty‐two children (24 boys, 18 girls) were enrolled between December 2013 and December 2015. Blood tests, including measurement of serum free carnitine via the enzyme cycling method, and acylcarnitine analysis on MS/MS of dried blood spot (DBS), were performed for the evaluation of nutrition status.ResultsMedian patient age was 2 years (range, 2 months–14 years). Mean serum free carnitine was 41.8 ± 19.2 μmol/L. In six of the 42 patients, serum free carnitine was <20 μmol/L (range, 4.0–18.7 μmol/L). C0 and C5‐OH measured on MS/MS of DBS were 33.8 ± 20.2 nmol/mL and 0.48 ± 0.22 nmol/mL, respectively. There was a strong positive correlation (r = 0.89, P < 0.001) between serum free carnitine and C0 measured on the same day. In one patient on hydrolyzed formula, C5‐OH was >1.00 nmol/L. Therapy‐resistant eczema was improved by treatment with additional biotin and a non‐hydrolyzed formula.ConclusionC0 and C5‐OH, measured on MS/MS of DBS, were useful for screening carnitine and biotin deficiencies.
Detection of the Excised, Damage‐containing Oligonucleotide Products of Nucleotide Excision Repair in Human Cells
Authors: Song Jimyeong , Kemp Michael G. , Choi Jun‐Hyuk 
Published: September 2016

AbstractThe human nucleotide excision repair system targets a wide variety of DNA adducts for removal from DNA, including photoproducts induced by UV wavelengths of sunlight. A key feature of nucleotide excision repair is its dual incision mechanism, which results in generation of a small, damage‐containing oligonucleotide approximately 24 to 32 nt in length. Detection of these excised oligonucleotides using cell‐free extracts and purified proteins with defined DNA substrates has provided a robust biochemical assay for excision repair activity in vitro. However, the relevance of a number of in vitro findings to excision repair in living cells in vivo has remained unresolved. Over the past few years, novel methods for detecting and isolating the excised oligonucleotide products of repair in vivo have therefore been developed. Here we provide a basic outline of a sensitive and versatile in vivo excision assay and discuss how the assay both confirms previous in vitro findings and offers a number of advantages over existing cell‐based DNA repair assays. Thus, the in vivo excision assay offers a powerful tool for readily monitoring the repair of DNA lesions induced by a large number of environmental carcinogens and anticancer compounds.
Implementing Propensity Score Matching with Network Data: The Effect of the General Agreement on Tariffs and Trade on Bilateral Trade
Authors: Arpino Bruno , De Benedictis Luca , Mattei Alessandra 
Published: September 2016

SummaryMotivated by the evaluation of the causal effect of the General Agreement on Tariffs and Trade on bilateral international trade flows, we investigate the role of network structure in propensity score matching under the assumption of strong ignorability. We study the sensitivity of causal inference with respect to the presence of characteristics of the network in the set of confounders conditionally on which strong ignorability is assumed to hold. We find that estimates of the average causal effect are highly sensitive to the node level network statistics in the set of confounders. Therefore, we argue that estimates may suffer from omitted variable bias when the network information is ignored, at least in our application.
Late Jurassic to Cretaceous evolution of the eastern Tethyan Hawasina Basin (Oman Mountains)
Authors: Wohlwend Stephan , Celestino Ricardo , Reháková Daniela , Huck Stefan , Weissert Helmut 
Published: September 2016

AbstractRemnants of a Mesozoic continental margin can be studied today in the nappe pile of the Oman Mountains. Successions of the Arabian carbonate platform and the adjacent deep Hawasina Basin are preserved in the nappe pile and in the foothills of this Mountain range. The Jurassic–Cretaceous sediment successions of the Hawasina Basin (Sumeini and Hamrat Duru Group) are focus of this study. These basinal archives contain information on the response of an eastern Tethyan equatorial ocean system to multiple perturbations of the carbon cycle and of climate during the Cretaceous. Turbiditic continental slope and basinal successions formed near the Calcite Compensation Depth are difficult to date with biostratigraphy and sequence stratigraphy. The available stratigraphic framework for the Hawasina successions was not sufficient for tracing palaeoceanography through the time window of interest in this study. Therefore, existing sequence stratigraphy and biostratigraphy are complemented by additional biostratigraphic data and with a newly established carbon and strontium isotope chemostratigraphy. The Hawasina Basin was affected by sea‐level variations, by changes in oceanography and also by regional tectonics. A first major modification of oceanography occurred at the end of the Jurassic when pelagic Maiolica‐type sediments were accumulated in the deep basin and on adjacent submarine highs (Lower Member of Huwar and Sid'r formations). Pelagic to hemipelagic conditions existed until the Valanginian, marked by a major carbon isotope excursion. Pelagic sediments were replaced afterwards by a succession of fine to coarse‐grained turbidites of Hauterivian to Aptian age. The transition into the mid‐Cretaceous is marked by a sudden shift to fine‐grained siliceous or chert deposits, at a time when sediments enriched in organic carbon were accumulated in the western Tethys and Atlantic Oceans. The continental slope as well as the Hawasina Basin seemed to have been well‐ventilated during Early and mid‐Cretaceous time. Siliceous limestones and chert are indicators of well‐mixed and nutrient‐rich surface water, while the absence of black shales suggests young and oxygenated deep water with a possible source on the vast Arabian platform. These peculiar oceanographic conditions were most pronounced during the onset of the extreme greenhouse episodes of the Oceanic Anoxic Event 1a.
Chemokine Patterns in Children with Acute Bacterial Infections
Authors: Cavalcanti N. V. , Torres L. C. , da Matta M. C. , Lindoso C. D. , A. Carvalho L. N. , Duarte M. C. M. B. , Correia J. B. 
Published: September 2016

AbstractChemokines are chemotactic cytokines that are mainly involved in the migratory patterns of immune cells. Few studies have evaluated the levels of chemokines in children with acute bacterial infections. The aim of this study was to evaluate the serum levels of chemokines MCP‐1, RANTES, MIG and IP‐10 in children with sepsis, community‐acquired pneumonia (CAP) and skin abscess. Serum levels of MCP‐1, RANTES, MIG and IP‐10 were measured in 37 children with sepsis, 27 children with CAP, 25 children with skin abscess and 20 controls with no signs of infection. Patients with sepsis, CAP and skin abscess had higher concentrations of RANTES compared to controls (P = 0.0057, P = 0.0004 and P = 0.0108, respectively). IP‐10 values were higher in patients with sepsis compared to children with skin abscess (P = 0.0075). However, MCP‐1 levels were lower in septic patients compared to controls (P = 0.0136). There was no difference on MIG concentrations between the groups. Our original findings observed that RANTES was consistently elevated in all types of infections suggesting this chemokine may play an important role in the pathogenesis of bacterial infection. Additionally, patients with sepsis had a unique pattern of response with high levels of IP‐10 but low levels of MCP‐1, which should be further explored as the markers of disease severity.
Selection of GP. Mur antigen‐negative RBC for blood recipients with anti‐‘Mia’ records decreases transfusion reaction rates in Taiwan
Authors: Yang C.‐A. , Lin J.‐A. , Chang C.‐W. , Wu K.‐H. , Yeh S.‐P. , Ho C.‐M. , Chang J.‐G. 
Published: September 2016

ABSTRACTObjectivesTo evaluate the clinical significance of GP. Mur antigen‐negative blood selection for transfusion in patients with anti‐‘Mia’ records.BackgroundThe GP. Mur RBC phenotype is prevalent (7·3%) in Taiwan. Antibodies against GP. Mur (anti‐‘Mia’) are identified in 1·24% of our population, and anti‐‘Mia’ screening using GP. Mur RBC has been routine for Taiwan's blood banks. However, due to the lack of commercial antibodies, only cross‐matching was used to prevent transfusion of GP. Mur‐positive blood to patients with anti‐‘Mia’ in most hospitals. There is still a risk of GP. Mur‐positive RBC exposure and subsequent anti‐‘Mia’‐related transfusion reactions.MethodsSince February 2014, GP. Mur antigen‐negative RBCs identified by reaction with anti‐‘Mia’‐positive serum were selected for blood recipients with anti‐‘Mia’ records. The transfusion reactions between January 2013 and January 2014 were compared with those that occurred between February 2014 and July 2015.ResultsThe transfusion reaction rate was significantly higher in anti‐‘Mia’‐positive blood recipients compared to total subjects receiving an RBC transfusion before GP. Mur‐negative donor RBC selection. After antigen‐negative RBC selection, the transfusion reaction frequency in subjects with anti‐‘Mia’ became similar to total blood recipients. IgG form anti‐‘Mia’ antibodies were present in all cases of probable anti‐‘Mia’‐related transfusion reactions. The time required for anti‐‘Mia’ boosting after transfusion was around 4–21 days.ConclusionSelection of GP. Mur‐negative RBC for transfusion to patients with anti‐‘Mia’ records could decrease the rate of transfusion reaction and antibody boosting. This procedure should be incorporated into blood bank routines in areas where anti‐‘Mia’ is prevalent.
Knowledge, attitudes and practices towards blood donation in Barbados
Authors: Atherley, A. E. , Taylor C. G. , Whittington A. , Jonker C. 
Published: September 2016

AbstractObjectiveTo obtain information to devise strategies for a voluntary blood donor mobilisation campaign in Barbados.BackgroundThe World Health Organization (WHO) recommends that 100% blood should be collected from voluntary non‐remunerated donors (VNRD), yet the majority of blood donations (75%) in Barbados are family/replacement donations. Increasing VNRD is paramount to achieving a safe, reliable blood supply, and understanding the population is a strategy suggested by the WHO to inform donor recruitment and education.MethodsParticipants in Barbados (n = 429) completed a self‐administered questionnaire in 2014. The questionnaire comprised 31 questions, including demographics (age, gender, highest educational attainment) and blood donation‐related knowledge, attitudes and practices. Analysis of variance, t‐test and linear regression were used to analyse data.ResultsA total of 53% (n = 219) of participants had previously donated blood; almost half were family/replacement donors, and over one‐third (36·2%) were lapsed donors and had not donated within the past 2 years. Knowledge deficits included blood donation requirements, deferral factors and maximum yearly donations. Most participants (79%) were willing to donate with more information. Participants with higher educational attainment and previous donors had higher total knowledge and attitude scores (P < 0·01). Single, female and younger participants were less likely to donate blood (P < 0·05).ConclusionsBarbados can likely increase voluntary blood donation rates by addressing knowledge deficits through education campaigns and increasing awareness of the need for donation.
Healthy donor hematopoietic stem cell mobilization with biosimilar granulocyte‐colony‐stimulating factor: safety, efficacy, and graft performance
Authors: Becker Petra , Schwebig Arnd , Brauninger Susanne , Bialleck Heike , Luxembourg Beate , Schulz Miriam , Tsamadou Chrysanthi , Wiesneth Markus , Reinhardt Peter , Mytilineos Joannis , Seidl Christian , Gattu Sreekanth , Kaliakina Natalia , Singh Pritibha , Schrezenmeier Hubert , Seifried Erhard , Bonig Halvard 
Published: September 2016

BACKGROUNDBiosimilar granulocyte‐colony‐stimulating factors (G‐CSFs) have been available in the European Union since 2008, and Sandoz' biosimilar filgrastim was approved in the United States in March 2015 for all of the reference product's indications except acute radiation syndrome. Biosimilar G‐CSFs have been largely embraced by the medical community, except for some reservations about healthy‐donor stem cell mobilization, for which use outside of clinical studies was cautioned against by some members of the scientific community.STUDY DESIGN AND METHODSIn a two‐center safety surveillance study (National Clinical Trial NCT01766934), 245 healthy volunteer stem cell donors were enrolled. Of 244 donors who began mobilization with twice‐daily Sandoz biosimilar filgrastim, 242 received a full (n = 241) or partial (n = 1) course of G‐CSF and underwent apheresis. Efficacy and safety were assessed and are reported here.RESULTSBiosimilar filgrastim was accompanied by the typical G‐CSF class‐related adverse effects of expected frequency and severity. Median mobilization for CD34‐positive stem cells was 97/µL (range, 20‐347/µL); after one apheresis (91%) or two aphereses (9%) from all but three donors (1.2%), cell doses in excess of the typical 4 × 106 CD34‐positive cells/kg of the recipient had been collected (range, 3‐52 × 106/kg). Biochemical and hematologic alterations were consistent with previous reports; all had normalized by the first follow‐up 1 month after mobilization. Stem cell products engrafted with typical probability and kinetics for G‐CSF‐mobilized stem cell products.CONCLUSIONThese data support the use of biosimilar filgrastim for healthy‐donor stem cell mobilization as safe and effective.