bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural bias in aggregated species‐level variables driven by repeated species co‐occurrences: a pervasive problem in community and assemblage data
Authors: Hawkins Bradford A. , Leroy Boris , Rodríguez Miguel Á. , Singer Alexander , Vilela Bruno , Villalobos Fabricio , Wang Xiangping , Zelený David 
Published: February 2017

AbstractAimSpecies attributes are often used to explain diversity patterns across assemblages/communities. However, repeated species co‐occurrences can generate spatial pattern and strong statistical relationships between aggregated attributes and richness in the absence of biological information. Our aim is to increase awareness of this problem.LocationNorth America.MethodsWe generated empirical species richness patterns using two data structures: (1) birds gridded from range maps and (2) tree communities from the US Forest Service's Forest Inventory and Analysis. We analysed richness using linear regression, regression trees, generalized additive models, geographically weighted regression and simultaneous autoregression, with ‘random intrinsic variables’ as predictors generated by assigning random numbers to species and calculating averages in assemblages. We then generated simulations in which species with cohesive or patchy distributions are placed with respect to the North American temperature gradient with or without a broad‐scale richness gradient. Random intrinsic variables are again used as predictors of richness. Finally, we analysed one simulated scenario with random intrinsic variables as both response and predictor variables.ResultsThe models of bird and tree richness often explained moderate to large proportions of the variance. Regression trees, geographically weighted regression and simultaneous autoregression were very sensitive to the problem; generalized additive models were moderately affected, as was multiple regression to a lesser extent. In the virtual data, the variance explained increased with increasing species co‐occurrences, but neither range cohesion, a richness gradient nor spatial autocorrelation in predictors had major impacts on the variance explained. The problem persisted when the response variable was also a random intrinsic variable.Main conclusionsRepeated species co‐occurrences can generate strong spurious relationships between richness and aggregated species attributes. It is important to realize that models utilizing assemblage variables aggregated from species‐level values, as well as maps illustrating their spatial patterns, cannot be taken at face value.
The strain‐dependent spatial evolution of garnet in a high‐P ductile shear zone from the Western Gneiss Region (Norway): a synchrotron X‐ray microtomography study
Authors: Macente A. , Fusseis F. , Menegon L. , Xiao X. , John T. 
Published: February 2017

AbstractReaction and deformation microfabrics provide key information to understand the thermodynamic and kinetic controls of tectono‐metamorphic processes, however, they are usually analysed in two dimensions, omitting important information regarding the third spatial dimension. We applied synchrotron‐based X‐ray microtomography to document the evolution of a pristine olivine gabbro into a deformed omphacite–garnet eclogite in four dimensions, where the 4th dimension is represented by the degree of strain. In the investigated samples, which cover a strain gradient into a shear zone from the Western Gneiss Region (Norway), we focused on the spatial transformation of garnet coronas into elongated garnet clusters with increasing strain. The microtomographic data allowed quantification of garnet volume, shape and spatial arrangement evolution with increasing strain. The microtomographic observations were combined with light microscope and backscatter electron images as well as electron microprobe (EMPA) and electron backscatter diffraction (EBSD) analysis to correlate mineral composition and orientation data with the X‐ray absorption signal of the same mineral grains. With increasing deformation, the garnet volume almost triples. In the low‐strain domain, garnet grains form a well interconnected large garnet aggregate that develops throughout the entire sample. We also observed that garnet coronas in the gabbros never completely encapsulate olivine grains. In the most highly deformed eclogites, the oblate shapes of garnet clusters reflect a deformational origin of the microfabrics. We interpret the aligned garnet aggregates to direct synkinematic fluid flow, and consequently influence the transport of dissolved chemical components. EBSD analyses reveal that garnet shows a near‐random crystal preferred orientation that testifies no evidence for crystal plasticity. There is, however evidence for minor fracturing, neo‐nucleation and overgrowth. Microprobe chemical analysis revealed that garnet compositions progressively equilibrate to eclogite facies, becoming more almandine‐rich. We interpret these observations as pointing to a mechanical disintegration of the garnet coronas during strain localization, and their rearrangement into individual garnet clusters through a combination of garnet coalescence and overgrowth while the rock was deforming.
Gemfibrozil, food and drug administration‐approved lipid‐lowering drug, increases longevity in mouse model of late infantile neuronal ceroid lipofuscinosis
Authors: Ghosh Arunava , Rangasamy Suresh Babu , Modi Khushbu K. , Pahan Kalipada 
Published: February 2017

AbstractLate Infantile Neuronal Ceroid Lipofuscinosis (LINCL) is a rare neurodegenerative disease caused by mutations in the Cln2 gene that leads to deficiency or loss of function of the tripeptidyl peptidase 1 (TPP1) enzyme. TPP1 deficiency is known to cause the accumulation of autofluoroscent lipid‐protein pigments in brain. Similar to other neurodegenerative disorders, LINCL is also associated with neuroinflammation and neuronal damage. Despite investigations, no effective therapy is currently available for LINCL. Therefore, we administered gemfibrozil (gem), an food and drug administration (FDA)‐approved lipid‐lowering drug, which has been shown to stimulate lysosomal biogenesis and induce anti‐inflammation, orally, at a dose of 7.5 mg/kg body wt/day to Cln2(−/−) mice. We observed that gem‐fed Cln2(−/−) mice lived longer by more than 10 weeks and had better motor activity compared to vehicle (0.1% Methyl cellulose) treatment. Gem treatment lowered the burden of storage materials, increased anti‐inflammatory factors like SOCS3 and IL‐1Ra, up‐regulated anti‐apoptotic molecule like phospho‐Bad, and reduced neuronal apoptosis in the brain of Cln2(−/−) mice. Collectively, this study reinforces a neuroprotective role of gem that may be of therapeutic interest in improving the quality of life in LINCL patients.
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Contemporary analysis of maternal and neonatal morbidity after uterine rupture: A nationwide population‐based study
Authors: Vilchez Gustavo , Dai Jing , Kumar Komal , Lagos Moraima , Sokol Robert J. 
Published: February 2017

AbstractAimUterine rupture is a rare but feared perinatal event. Despite abundant research and changes to guidelines implemented to reduce this complication, evaluation of whether uterine rupture still engenders significant maternal/neonatal morbidity has not been conducted. We analyzed recent cases of maternal/neonatal morbidity after uterine rupture.MethodsDeliveries complicated by uterine rupture from 2011 to 2012 in the United States were selected. Comparison cases without uterine rupture were used as controls. Measures of maternal/neonatal complications were compared with χ2 test, and relative risks were calculated. Logistic regression was used to identify the most significant complications. P < 0.05 indicated statistical significance.ResultsFrom 7 922 016 births, 1925 cases of uterine rupture and 3765 controls were identified. Regression models retained four maternal outcomes; blood transfusion was the most common (~15%) and unplanned hysterectomy had the highest odds (~97‐fold). For newborns, the model retained three measures of morbidity; neonatal intensive care unit admission was the most common (~35%) and seizures had the highest odds (~20‐fold).ConclusionsDespite efforts to reduce complications, mothers remain at significant risk of unplanned hysterectomy and intensive care unit admission. Neonates are at sizeable risk for neonatal intensive care unit admission and seizures, recognized markers of long‐term neurobehavioral abnormality. Uterine rupture remains a major risk for mothers and babies.
Apple Replant Disorder of Pingyitiancha Rootstock is Closely Associated with Rhizosphere Fungal Community Development
Authors: Sun Jian , Zhang Qiang , Li Xingliang , Zhou Beibei , Wei Qinping 
Published: February 2017

AbstractThe aim of this study was to examine rhizosphere fungal community development in apple replant soil and a new planting soil in Beijing through a potted experiment with the apomictic triploid Pingyitiancha rootstock using the Illumina Miseq method. Steam sterilization significantly enhanced seedling growth in replant soil, while root segment addition did not enhance replant disease symptoms. The bulk soil of the replant site (ReSoil) and the new soil of the planting site (NewSoil) were sampled prior to nursery planting, and rhizosphere soils were r Qinping esampled after one growing season as RePlant and NewPlant, respectively. Approximately 48.3, 47.9, 59.8 and 68.8% of the operational taxonomic units (OTUs) were classified as Ascomycota and Basidiomycota in the community of ReSoil, New Soil, RePlant and NewPlant, respectively. Shannon indices suggested that planting apple nurseries increased the fungal diversity of rhizosphere soil in both soils. Apple replant disorder (ARD) was highly associated with an unbalanced microbial ecosystem with more saprophytic and pathogenic fungi, but less species known to produce antimicrobial metabolites, while Rhizopus, Pyrenochaeta and Eurotium were identified as the key factors in ARD.
Role of PIN1 on in vivo periodontal tissue and in vitro cells
Authors: Park K.‐H. , Cho E.‐H. , Bae W.‐J. , Kim H.‐S. , Lim H.‐C. , Park Y.‐D. , Lee M.‐O. , Cho E.‐S. , Kim E.‐C. 
Published: February 2017

BackgroundAlthough expression of peptidyl‐prolyl cis/trans isomerase NIMA‐interacting 1 (PIN1) was reported in bone tissue, the precise role of PIN1 in periodontal tissue and cells remain unclear.Material & MethodsTo elucidate the roles of PIN1 in periodontal tissue, its expression in periodontal tissue and cells, and effects on in vitro 4 osteoblast differentiation and the underlying signaling mechanisms were evaluated.ResultsPIN1 was expressed in mouse periodontal tissues including periodontal ligament cells (PDLCs), cementoblasts and osteoblasts at the developing root formation stage (postnatal, PN14) and functional stage of tooth (PN28). Treatment of PIN1 inhibitor juglone, and gene silencing by RNA interference promoted osteoblast differentiation in PDLCs and cementoblasts, whereas the overexpression of PIN1 inhibited. Moreover, osteogenic medium‐induced activation of AMPK, mTOR, Akt, ERK, p38 and NF‐jB pathways were enhanced by PIN1 siRNA, but attenuated by PIN1 overexpression. Runx2 expressions were induced by PIN1 siRNA, but downregulated by PIN1 overexpression.ConclusionIn summary, this study is the first to demonstrate that PIN1 is expressed in developing periodontal tissue, and in vitro PDLCs and cementoblasts. PIN1 inhibition stimulates osteoblast differentiation, and thus may play an important role in periodontal regeneration.
Comparison of the spread of two different volumes of contrast medium when performing ultrasound‐guided transversus abdominis plane injection in dog cadavers
Authors: Zoff A. , Laborda‐Vidal P. , Mortier J. , Amengual M. , Rioja E. 
Published: February 2017

ObjectivesTo compare, via CT imaging, the spread of different volumes of diluted iodinated contrast medium in the transversus abdominis muscle plane of dog cadavers.
Methods
Prospective, randomised study. An electro stimulation or a SonoTAP needle was inserted in plane with the ultrasound beam in the fascia between the internal oblique and transversus abdominis muscles. A test dose of 1 ml of diluted contrast (30 mg/mL iohexol) was injected to confirm positioning, followed by 0
·
5 mL/kg (n=14) or 1 mL/kg (n=12) and the distribution of the fluid compared.
Results
Contrast medium was identified exclusively in the transversus abdominis plane in 19 of 26 dogs. In one dog, the contrast lay between the external and internal oblique muscles and partially in three dogs. Intraperitoneal contrast was detected in 6 of 26 dogs (23%). No significant differences were found in the dorso‐ventral or cranio‐caudal spread or area of distribution but a significant difference was found in the transverse spread. There was an association between poor ultrasound visualisation of the tip of the needle and intraperitoneal injection.
Clinical Significance
Injection of 1 mL/kg of diluted contrast did not result in wider cranio‐caudal spread in the transversus abdominis muscle plane of dog cadavers when compared with 0
·
5 mL/kg. Intraperitoneal injection is a risk and might be reduced with good needle visualisation.
Hepatitis B surface antigen reduction by switching from long‐term nucleoside/nucleotide analogue administration to pegylated interferon
Authors: Tamaki N. , Kurosaki M. , Kusakabe A. , Orito E. , Joko K. , Kojima Y. , Kimura H. , Uchida Y. , Hasebe C. , Asahina Y. , Izumi N. ,   Japanese Red Cross Hospital Liver Study Group
Published: February 2017

SummaryHepatitis B surface antigen (HBsAg) reduction during nucleoside/nucleotide analogue (NA) therapy is slow and an alternative strategy for patients receiving ongoing NA to facilitate HBsAg reduction is required. We investigated whether switching to pegylated interferon (PEG‐IFN) after long‐term NA administration enhances HBsAg reduction. Forty‐nine patients who switched from long‐term NA to 48 weeks of PEG‐IFN alfa‐2a were studied. The mean duration of previous NA was 48 months (sequential group). A total of 147 patients who continued NA and matched for baseline characteristics were analysed for comparison (NA continuation group). The treatment response was defined as HBsAg reduction ≥1.0 logIU/mL at the end of PEG‐IFN. HBsAg reduction at week 48 was 0.81±1.1 logIU/mL in the sequential group, which was significantly higher than that in the NA continuation group (0.11±0.3 logIU/mL, P < .001). The treatment response was achieved in 29% and 2% of the sequential group and NA continuation group (P < .001), and the odds ratio of sequential therapy for the treatment response was 19 compared with the NA continuation (P < .001). In patients tested positive for hepatitis B e antigen (HBeAg), HBeAg seroconversion was higher in the sequential group (44% vs 8%, P < .001). In HBeAg‐negative patients, only patients in the sequential group achieved HBsAg loss. No patient needed to resume NA administration because of HBV DNA increase accompanied by alanine aminotransferase flares. In summary, sequential therapy with PEG‐IFN after long‐term NA enhances the reduction of HBsAg and may represent a treatment option to promote HBsAg loss.
A retrospective study of hepatitis B mother‐to‐child transmission prevention and postvaccination serological test results of infants at risk of perinatal transmission in two counties of middle China
Authors: Yonghao G. , Pumei D. , Jianhui Y. , Jin X. , Yanyang Z. , Zhe W. 
Published: February 2017

SummaryApproximately, 240 million people have chronic hepatitis B worldwide, with mother‐to‐child‐transmission (MTCT) accounting for most cases. Therefore, Henan Province, China launched a public health programme to preventMTCT. To determine the efficacy of this health programme, a survey was carried out in Huixian and Xinan counties, which are located in northern and western Henan. All infants born in these two counties between January 1, 2013 and March 31, 2014 to a mother positive for hepatitis B surface antigen (HBsAg) were surveyed. In total, there were 438 mother‐infant pairs. A blood sample was collected from all mothers and infants and the following Hepatitis B virus (HBV) markers, antibodies, and antigens were measured:HBsAg, anti‐HBs, anti‐HBc,HBeAg, anti‐HBe, andHBV‐DNA. All mothers and 5.3% (23/438) of the infants wereHBsAg positive. All infants received three doses of the hepatitis B vaccine (HepB) and the postvaccination serological test (PVST) showed that the appropriate interval forPVSTmay be 1‐8 months after the final HepB dose. Multivariable analysis showed that infants without a timely first and second dose of the HepB, with anHBeAg‐positive mother and mothers who had not received hepatitis B immune globulin during pregnancy were implicated inMTCT. The stratified analysis using maternalHBeAg as a marker showed that maternalHBeAg may be a strong risk factor forMTCT. To preventMTCTin middle China, several courses of action are recommended. The first is to optimize the screening method for the mother to allowHBeAg andHBsAg‐positive mothers to receive medical treatment during pregnancy and a timely birth dose of the vaccine to all infants. Second, all infants with anHBsAg‐positive mother should be tested for anti‐HBs andHBsAg at 7‐14 months old and any anti‐HBs‐nonresponse infants should receive an additional three dosesof the vaccine.
Comparative efficacy of metoclopramide, ondansetron and maropitant in preventing parvoviral enteritis‐induced emesis in dogs
Authors: Yalcin E. , Keser G. O. 
Published: February 2017

The aim of the study was to evaluate the efficiencies of selected anti‐emetic drugs (metoclopramide, ondansetron and maropitant) in preventing vomiting in the treatment of canine parvoviral enteritis. We designed a randomized, prospective clinical study. PVE quick ELISA test‐positive dogs between 4 and 12 months of age were included in the study. Each of metoclopramide, ondansetron, maropitant and control group had 8 dogs. Metoclopramide and ondansetron were administered as 0.5 mg/kg doses three times a day via intravenous route, and maropitant was administered as 1 mg/kg doses once a day subcutaneously. The number and severity of daily vomitings were recorded. All dogs were treated and monitored for five days; treatments were continued until all animals healed. Metoclopramide, ondansetron and maropitant decreased the severity of vomiting from the first day and the vomiting numbers from the third day in PVE treatment. Obtained results showed that maropitant can be used successfully such as metoclopramide and ondansetron, which are frequently used for PVE treatment. At the same time, it was discovered that metoclopramide, ondansetron and maropitant were equally effective in reducing the frequency and severity of vomiting.
Corpus Use in Language Learning: A Meta‐Analysis
Authors: Boulton Alex , Cobb Tom 
Published: February 2017

AbstractThis study applied systematic meta‐analytic procedures to summarize findings from experimental and quasi‐experimental investigations into the effectiveness of using the tools and techniques of corpus linguistics for second language learning or use, here referred to as data‐driven learning (DDL). Analysis of 64 separate studies representing 88 unique samples reporting sufficient data indicated that DDL approaches result in large overall effects for both control/experimental group comparisons (d = 0.95) and for pre/posttest designs (d = 1.50). Further investigation of moderator variables revealed that small effect sizes were generally tied to small sample sizes. Research has barely begun in some key areas, and durability/transfer of learning through delayed posttesting remains an area in need of further investigation. Although DDL research demonstrably improved over the period investigated, further changes in practice and reporting are recommended.Open PracticesThis article has been awarded Open Materials and Open Data badges. All materials and data are publicly accessible via the Open Science Framework at https://osf.io/jkktw. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae)
Authors: Thornhill D. J. , Howells E. J. , Wham D. C. , Steury T. D. , Santos S. R. 
Published: February 2017

AbstractSymbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broadscale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine‐scale population structure and biogeography of these dinoflagellates. Yet population‐level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic‐driven global climate change impacts these symbionts and their host associations. Here, we present a synthesis of population‐level characteristics for Symbiodinium, with an emphasis on how phylogenetic affinities, dynamics within and among host individuals, and a propensity towards clonality shape patterns on and across reefs. Major inferences include the following: (i) Symbiodinium populations within individual hosts are comprised mainly of cells belonging to a single or few genetic clones. (ii) Symbiont populations exhibit a mixed mode of reproduction, wherein at least one sexual recombination event occurs in the genealogy between most genotypes, but clonal propagation predominates overall. (iii) Mutualistic Symbiodinium do not perpetually persist outside their hosts, instead undergoing turnover and replacement via the continuous shedding of viable clonal cells from host individuals. (iv) Symbiont populations living in the same host, but on different reefs, are often genetically subdivided, suggesting low connectivity, adaptation to local conditions, or prolific asexual reproduction and low effective population sizes leading to disproportionate success within and among hosts. Overall, this synthesis forms a basis for future investigations of coral symbiosis ecology and evolution as well as delimitation of species boundaries in Symbiodinium and other eukaryotic microorganisms.
Next‐generation transgenic cotton: pyramiding RNAi and Bt counters insect resistance
Authors: Ni Mi , Ma Wei , Wang Xiaofang , Gao Meijing , Dai Yan , Wei Xiaoli , Zhang Lei , Peng Yonggang , Chen Shuyuan , Ding Lingyun , Tian Yue , Li Jie , Wang Haiping , Wang Xiaolin , Xu Guowang , Guo Wangzhen , Yang Yihua , Wu Yidong , Heuberger Shannon , Tabashnik Bruce E. , Zhang Tianzhen , Zhu Zhen 
Published: February 2017

SummaryTransgenic crops producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) are extensively cultivated worldwide. To counter rapidly increasing pest resistance to crops that produce single Bt toxins, transgenic plant ‘pyramids’ producing two or more Bt toxins that kill the same pest have been widely adopted. However, cross‐resistance and antagonism between Bt toxins limit the sustainability of this approach. Here we describe development and testing of the first pyramids of cotton combining protection from a Bt toxin and RNA interference (RNAi). We developed two types of transgenic cotton plants producing double‐stranded RNA (dsRNA) from the global lepidopteran pest Helicoverpa armigera designed to interfere with its metabolism of juvenile hormone (JH). We focused on suppression of JH acid methyltransferase (JHAMT), which is crucial for JH synthesis, and JH‐binding protein (JHBP), which transports JH to organs. In 2015 and 2016, we tested larvae from a Bt‐resistant strain and a related susceptible strain of H. armigera on seven types of cotton: two controls, Bt cotton, two types of RNAi cotton (targeting JHAMT or JHBP) and two pyramids (Bt cotton plus each type of RNAi). Both types of RNAi cotton were effective against Bt‐resistant insects. Bt cotton and RNAi acted independently against the susceptible strain. In computer simulations of conditions in northern China, where millions of farmers grow Bt cotton as well as abundant non‐transgenic host plants of H. armigera, pyramided cotton combining a Bt toxin and RNAi substantially delayed resistance relative to using Bt cotton alone.