bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of inundation and drought on eukaryote biodiversity in semi‐arid floodplain soils
Authors: Baldwin Darren S. , Colloff Matthew J. , Rees Gavin N. , Chariton Anthony A. , Watson Garth O. , Court Leon N. , Hartley Diana M. , Morgan Matthew j. , King Andrew J. , Wilson Jessica S. , Hodda Michael , Hardy Christopher M. 
Published: February 2013

AbstractFloodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi‐arid floodplain would transition towards comprising mainly dry‐soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post‐flood) were dominated by persistent rather than either aquatic or dry‐specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post‐flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post‐flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi‐arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.
Assessment of spatial discordance of primary and effective seed dispersal of European beech (Fagus sylvatica L.) by ecological and genetic methods
Authors: Millerón M. , López de Heredia U. , Lorenzo Z. , Alonso J. , Dounavi A. , Gil L. , Nanos N. 
Published: February 2013

AbstractSpatial discordance between primary and effective dispersal in plant populations indicates that postdispersal processes erase the seed rain signal in recruitment patterns. Five different models were used to test the spatial concordance of the primary and effective dispersal patterns in a European beech (Fagus sylvatica) population from central Spain. An ecological method was based on classical inverse modelling (SSS), using the number of seed/seedlings as input data. Genetic models were based on direct kernel fitting of mother‐to‐offspring distances estimated by a parentage analysis or were spatially explicit models based on the genotype frequencies of offspring (competing sources model and Moran‐Clark's Model). A fully integrated mixed model was based on inverse modelling, but used the number of genotypes as input data (gene shadow model). The potential sources of error and limitations of each seed dispersal estimation method are discussed. The mean dispersal distances for seeds and saplings estimated with these five methods were higher than those obtained by previous estimations for European beech forests. All the methods show strong discordance between primary and effective dispersal kernel parameters, and for dispersal directionality. While seed rain was released mostly under the canopy, saplings were established far from mother trees. This discordant pattern may be the result of the action of secondary dispersal by animals or density‐dependent effects; that is, the Janzen‐Connell effect.
An approach to identify putative hybrids in the ‘coalescent stochasticity zone’, as exemplified in the African plant genus Streptocarpus (Gesneriaceae)
Authors: de Villiers Margaret J. , Pirie Michael D. , Hughes Mark , Möller Michael , Edwards Trevor J. , Bellstedt Dirk U. 
Published: February 2013

Summary

The inference of phylogenetic relationships is often complicated by differing evolutionary histories of independently‐inherited markers. The causes of the resulting gene tree incongruence can be challenging to identify, often relying on coalescent simulations dependent on unverifiable assumptions. We investigated alternative techniques using the South African rosulate species of Streptocarpus as a study group.

Two independent gene trees – from the nuclear ITS region and from three concatenated plastid regions (trnL‐F, rpl20‐rps12 and trnC‐D) – displayed widespread, strongly supported incongruence. We investigated the causes by detecting genetic exchange across morphological borders using morphological optimizations and genetic exchange across species boundaries using the genealogical sorting index.

Incongruence between gene trees was associated with ancestral shifts in growth form (in four species) but not in pollination syndrome, suggesting introgression limited by reproductive barriers. Genealogical sorting index calculations showed polyphyly of two additional species, while individuals of all others were significantly associated. In one case the association was stronger according to the internal transcribed spacer data than according to the plastid data, which, given the smaller effective population size of the plastid, may also indicate introgression.

These approaches offer alternative ways to identify potential hybridization events where incomplete lineage sorting cannot be rejected using simulations.
Associations of postnatal growth with asthma and atopy: the PROBIT Study
Authors: Anderson Emma L. , Fraser Abigail , Martin Richard M. , Kramer Michael S. , Oken Emily , Patel Rita , Tilling Kate 
Published: February 2013

AbstractBackgroundIt has been hypothesised that postnatal weight and length/height gain are variously related to wheeze, asthma and atopy; however, supporting evidence is limited and inconsistent.MethodsWeights and lengths/heights of 12,171 term infants were measured from birth to 12 months and at 6.5 yr and extracted from polyclinic records prospectively obtained between 12 and 60 months. Atopic phenotypes were ascertained at 6.5 yr with the International Study of Asthma and Allergy in Childhood questionnaire and skin prick tests. Logistic regression models investigated whether rates of weight and length/height gain from infancy to mid‐childhood were associated with atopy phenotypes that have occurred ever or in the last 12 months.ResultsAfter controlling for confounders and prior weight and length/height gain, all weight gain variables except birth weight were positively associated with ever having wheezed (p < 0.1). A one s.d. increase in weight gain rate between 0 and 3 months was associated with a 12% increase (2–23%) in allergic rhinitis ever. No other consistent patterns of association were found for weight gain or length/height gain rate between 0 and 60 months with atopic outcomes at 6.5 yr. In contrast, all atopy outcomes except for ever having asthma were associated with current weight and height, even after controlling for prior growth.ConclusionCurrent height and weight are more strongly associated with the development of atopic phenotypes in childhood than patterns of infant and early childhood growth, which may well reflect reverse causality (atopy effects on growth) or residual confounding by an unknown common cause of growth and atopy.
The Social Construction of Race and Minorities in Japan
Authors: Yamashiro Jane H. 
Published: February 2013

AbstractThis article provides an overview of the state of the field of racial and other minorities in Japan – a field that has developed in English mostly since the 1990s. The construction of race in Japan conflates race, ethnicity, language, culture, class, and citizenship. As a result, the majority “Japanese” are constructed against “foreigners,” both categories implying the aforementioned characteristics. Minorities in Japan lack some or all of the aforementioned traits: most are seen as racially different from Japanese but some are marginalized in other ways that support hierarchical social organization. After reviewing scholarship that analyzes the meaning of race in Japan, I briefly describe the major minority groups: Ainu, Okinawans, Burakumin, ethnic Koreans, foreign workers, Japanese Brazilians and mixed race Japanese.
Conservation tillage systems: a review of its consequences for greenhouse gas emissions
Authors: Abdalla M. , Osborne B. , Lanigan G. , Forristal D. , Williams M. , Smith P. , Jones M. B. 
Published: February 2013

AbstractConservation tillage (CT) is an umbrella term encompassing many types of tillage and residue management systems that aim to achieve sustainable and profitable agriculture. Through a global review of CT research, the objective of this paper was to investigate the impacts of CT on greenhouse gas (GHG) emissions. Based on the analysis presented, CT should be developed within the context of specific climates and soils. A number of potential disadvantages in adopting CT practices were identified, relating mainly to enhanced nitrous oxide emissions, together with a number of advantages that would justify its wider adoption. Almost all studies examined showed that the adoption of CT practices reduced carbon dioxide emissions, while also contributing to increases in soil organic carbon and improvements in soil structure.
Effects of critical source area on sediment yield and streamflow
Authors: Pradhanang Soni M. , Briggs Russell D. 
Published: February 2013

AbstractThe spatial discretization scale determines the degree to which the spatial heterogeneity of the surface condition and the stream network can be represented. Discretization scale can have a significant impact on watershed model results, with respect to both hydrology and water quality. The impact of critical source area (CSA) on simulated water yield for each cell can be assessed for streamflow and run‐off using the Annualized Agricultural Non‐Point Source (AnnAGNPS) model. The total number of cells simulated for the six watersheds ranged from 8 to 352 for various CSA combinations. Increasing the number of subwatersheds increased water and sediment yield in many watersheds. Increasing the number of cells influences the depiction of land use and soil type accordingly and therefore influences run‐off. The applied CSAs were also compared with topographic parameters such as average cell slope, average channel slope and length to width ratio of each watershed.
The water supply is fine: decision‐maker perceptions of water quantity and supply‐side management
Authors: Cockerill Kristan 
Published: February 2013

AbstractYears of research have called for more science to be integrated into water management decisions and for a shift from supply‐side to demand‐side management; yet, there remains a strong emphasis on supply‐side approaches and in many areas limited attention to hydrological data. A survey and interviews with decision‐makers in western North Carolina reveal that there is only low‐level concern about water quantity, and this drives a continued emphasis on supply‐side management and no perceived need for hydrological data. The historical realities of low demand and abundant water have generated a perception of ‘water supply’ as disconnected from physical, hydrological systems and allowed for ad hoc decision‐making processes to prevail. The lack of well‐established processes may, ironically, provide significant opportunities for employing collaboration among researchers and decision‐makers to develop policies and processes that integrate data into making water management decisions and thus prompt increased attention to water demand.
A GEOMETRIC STUDY OF WASSERSTEIN SPACES: HADAMARD SPACES
Authors: BERTRAND JÉRÔME , KLOECKNER BENOÎT 
Published: February 2013

Optimal transport enables one to construct a metric on the set of (sufficiently small at infinity) probability measures on any (not too wild) metric space X, called its Wasserstein space [Formula: see text]. In this paper we investigate the geometry of [Formula: see text] when X is a Hadamard space, by which we mean that X has globally non-positive sectional curvature and is locally compact. Although it is known that, except in the case of the line, [Formula: see text] is not non-positively curved, our results show that [Formula: see text] have large-scale properties reminiscent of that of X. In particular we define a geodesic boundary for [Formula: see text] that enables us to prove a non-embeddablity result: if X has the visibility property, then the Euclidean plane does not admit any isometric embedding in [Formula: see text].
Biases in Expendable Bathythermograph Data: A New View Based on Historical Side-by-Side Comparisons
Authors: Cowley Rebecca , Wijffels Susan , Cheng Lijing , Boyer Tim , Kizu Shoichi 
Published: February 2013

Abstract
Because they make up 56% of ocean temperature profile data between 1967 and 2001, quantifying the biases in expendable bathythermograph (XBT) data is fundamental to understanding the evolution of the planetary energy and sea level budgets over recent decades. The nature and time history of these biases remain in dispute and dominate differences in analyses of the history of ocean warming. A database of over 4100 side-by-side deployments of XBTs and conductivity–temperature–depth (CTD) data has been assembled, and this unique resource is used to characterize and separate out the pure temperature bias from depth error in a way that was not previously possible. Two independent methods of bias extraction confirm that the results are robust to bias model and fitting method. It was found that there is a pure temperature bias in Sippican probes of ~0.05°C, independent of depth. The temperature bias has a time dependency, being larger (~0.1°C) in the earlier analog acquisition era and being likely due to changes in recorder type. Large depth errors are found in the 1970s–80s in shallower-measuring Sippican T4/T6 probe types, but the deeper-measuring Sippican T7/Deep Blue (DB) types have no error during this time. The Sippican T7/DB fall rate slows from ~1990 onward. It is found that year-to-year variations in fall rate have a bigger effect on corrections to the global XBT database than do any small effects of ocean temperature on fall rate. This study has large implications for the future development of better schemes to correct the global historical XBT archive.
Generalized Dunkl-Williams inequality in 2-inner product spaces
Authors: Najati Abbas , Saem M Mohammadi , Bae Jae-Hyeong 
Published: February 2013

Abstract
We consider the generalized Dunkl-Williams inequality in 2-normed spaces. Also, we give necessary and sufficient conditions for having the equality case in the strictly convex 2-normed space X.
Multilocus sequence analysis of Treponema denticolastrains of diverse origin
Authors: Mo Sisu , You Meng , Su Yvonne CF , Lacap-Bugler Donnabella C , Huo Yong-biao , Smith Gavin JD , Leung W Keung , Watt Rory M 
Published: February 2013

Abstract

Background
The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA) of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA.

Results
The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC) were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA) to 8.9% (dnaN). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain) using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level.

Conclusions
Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic analysis of T. denticola isolates, which will greatly assist future biological and epidemiological investigations involving this putative ‘periodontopathogen’.
Cloning and characterization of two Argonaute genes in wheat (Triticum aestivum L.)
Authors: Meng Fanrong , Jia Haiying , Ling Na , Xue Yinlei , Liu Hao , Wang Ketao , Yin Jun , Li Yongchun 
Published: February 2013

Abstract

Background
Argonaute proteins are key components of RNA interference (RNAi), playing important roles in RNA-directed gene silencing. Various classes of Argonaute genes have been identified from plants and might be involved in developmental regulation. However, little is known about these genes in wheat (Triticum aestivum).

Results
In this study, two full-length cDNAs of Argonaute were cloned from wheat, designated as TaAGO1b and TaAGO4. The cDNA of TaAGO1b is 3273 bp long and encodes 868 amino acids, with a predicted molecular weight of ~97.78 kDa and pI of 9.29. The 3157-bp TaAGO4 encodes 916 amino acids, with a molecular mass of 102.10 kDa and pI of 9.12. Genomics analysis showed that TaAGO1b and TaAGO4 contain 20 and 18 introns, respectively. Protein structural analysis demonstrated that typical PAZ and PIWI domains were found in both TaAGO1b and TaAGO4. From the highly conserved PIWI domains, we detected conserved Asp-Asp-His (DDH) motifs that function as a catalytic triad and have critical roles during the process of sequence-specific cleavage in the RNAi machinery. Structural modelling indicated that both TaAGOs can fold to a specific α/β structure. Moreover, the three aligned DDH residues are spatially close to each other at the “slicer” site of the PIWI domain. Expression analysis indicated that both genes are ubiquitously expressed in vegetative and reproductive organs, including the root, stem, leaf, anther, ovule, and seed. However, they are differentially expressed in germinating endosperm tissues. We were interested to learn that the two TaAGOs are also differentially expressed in developing wheat plants and that their expression patterns are variously affected by vernalization treatment. Further investigation revealed that they can be induced by cold accumulation during vernalization.

Conclusions
Two putative wheat Argonaute genes, TaAGO1b and TaAGO4, were cloned. Phylogenetic analysis, prediction of conserved domains and catalytic motifs, and modelling of their protein structures suggested that they encode functional Argonaute proteins. Temporal and spatial expression analyses indicated that these genes are potentially involved in developmental regulation of wheat plants.
Safety and efficacy of high-dose daptomycin as salvage therapy for severe gram-positive bacterial sepsis in hospitalized adult patients
Authors: Lai Chung-Chih , Sheng Wang-Huei , Wang Jann-Tay , Cheng Aristine , Chuang Yu-Chung , Chen Yee-Chun , Chang Shan-Chwen 
Published: February 2013

Abstract

Background
Increasing the dosage of daptomycin may be advantageous in severe infection by enhancing bactericidal activity and pharmacodynamics. However, clinical data on using daptomycin at doses above 6 mg/kg in Asian population are limited.

Methods
A retrospective observational cohort study of all hospitalized adult patients treated with daptomycin (> 6 mg/kg) for at least 72 hours was performed in Taiwan.

Results
A total of 67 patients (40 males) with a median age of 57 years received a median dose of 7.61 mg/kg (range, 6.03-11.53 mg/kg) of daptomycin for a median duration of 14 days (range, 3–53 days). Forty-one patients (61.2%) were in intensive care units (ICU). Sites of infections included complicated skin and soft tissue infections (n = 16), catheter-related bacteremia (n = 16), endocarditis (n = 11), primary bacteremia (n = 10), osteomyelitis and septic arthritis (n = 9), and miscellaneous (n = 5). The median Pitt bacteremia score among the 54 (80.6%) patients with bacteremia was 4. The most common pathogen was methicillin-resistant Staphylococcus aureus (n = 38). Fifty-nine patients (88.1%) were treated with daptomycin after glycopepetide use. Overall, 52 (77.6%) patients achieved clinical success. The all-cause mortality rate at 28 day was 35.8%. In multivariate analysis, the significant predictors of in-hospital mortality in 54 bacteremic patients were malignancies (P = 0.01) and ICU stay (P = 0.02). Adverse effects of daptomycin were generally well-tolerated, leading to discontinuation in 3 patients. Daptomycin-related creatine phosphokinase (CPK) elevations were observed in 4 patients, and all received doses > 8 mg/kg.

Conclusions
Treatment with high dose daptomycin as salvage therapy was generally effective and safe in Taiwan. CPK level elevations were more frequent in patients with dose > 8 mg/kg.
Lanthanum carbonate for the treatment of hyperphosphatemia in CKD 5D: multicenter, double blind, randomized, controlled trial in mainland China
Authors: Xu Jing , Zhang Yi-Xiang , Yu Xue-Qing , Liu Zhi-Hong , Wang Li-Ning , Chen Jiang-Hua , Fan Ya-Ping , Ni Zhao-Hui , Wang Mei , Yuan Fa-Huan , Ding Guo-Hua , Chen Xiang-Mei , Zhang Ai-Ping , Mei Chang-Lin 
Published: February 2013

Abstract

Background
Serum phosphorus control is critical for chronic kidney disease (CKD) 5D patients. Currently, clinical profile for an oral phosphorus binder in the mainland Chinese population is not available.

Objective
To establish the efficacy, safety, and tolerability of lanthanum carbonate in CKD 5D patients.

Design
Multicenter, randomized, double blind, placebo-controlled study. A central randomization center used computer generated tables to allocate treatments.

Setting
Twelve tertiary teaching hospitals and medical university affiliated hospitals in mainland China.

Participants
Overall, 258 hemodialysis or continuous ambulatory peritoneal dialysis (CAPD) adult patients were enrolled.

Intervention
After a 0–3-week washout period and a 4-week lanthanum carbonate dose-titration period, 230 patients were randomized 1:1 to receive lanthanum carbonate (1500 mg-3000 mg) or placebo for a further 4-week maintenance phase.

Main outcome measures
Efficacy and safety of lanthanum carbonate to achieve and maintain target serum phosphorus concentrations were assessed.

Results
In the titration phase, serum phosphorus concentrations of all patients decreased significantly. About three-fifths achieved target levels without significantly disturbing serum calcium levels. At the end of the maintenance period, the mean difference in serum phosphorus was significantly different between the lanthanum carbonate and placebo-treated groups (0.63±0.62 mmol/L vs. 0.15±0.52 mmol/L, P < 0.001). The drug-related adverse effects were mild and mostly gastrointestinal in nature.

Conclusion
Lanthanum carbonate is an efficacious and well-tolerated oral phosphate binder with a mild AE profile in hemodialysis and CAPD patients. This agent may provide an alternative for the treatment of hyperphosphatemia in CKD 5D patients in mainland China.

Trial registration
No. ChiCTR-TRC-10000817