bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic diversity reveals hidden patterns related to population source and species pools during restoration
Authors: Khalil Mohammed I. , Gibson David J. , Baer Sara G. 
Published: July 2016

Summary

A phylogenetic perspective of community assembly can reveal new insights into how variation within dominant species interacts with the local species pool to influence the structure of restored plant communities. Many studies have examined the effect of dominant species in structuring plant communities, but few have investigated their effect on phylogenetic diversity (PD).

We established grassland in a post‐agricultural field using two population sources (cultivars and local ecotypes) of three dominant grasses (Sorghastrum nutans, Andropogon gerardii and Schizachyrium scoparium) with three unique pools of subordinate species that varied in PD but not taxonomic or life‐form diversity. We tested the effect of the population source treatment on two metrics of community PD (net relatedness index [NRI] and nearest taxon index [NTI]) during the first 4 years of restoration. The NRI measures the overall pairwise phylogenetic distance between all pairs of taxa in a community. By contrast, NTI measures the pairwise distance between closely related taxa in a community.

Population sources had a transitory effect on community phylogenetic structure over time. Local ecotypes decreased the abundance of closely related eudicots, monocots (low +NRI and +NTI values) and volunteer species (−NTI) more than cultivars. However, population sources did not affect ecologically conservative species (i.e. species with intermediate‐to‐poor ecological tolerance and a high degree of fidelity to prairie habitats). Thus, cultivars might have a positive effect on community phylogenetic diversity more than local ecotypes by decreasing the abundance of a phylogenetically diverse community of less closely related volunteer species. Differences in PD of seed mixes were maintained in the community of high‐fidelity species, but did not affect PD of the unsown (volunteer) species in the assembling community.

Synthesis and applications. This is the first experiment to show consequences of using different seed sources on phylogenetic diversity (PD) in grassland restoration. Phylogenetics can reveal the effects of population sources on the abundance of volunteer species not evident through traditional analyses of species diversity. The PD of seed mixes or establishing communities, or other assessments of phylogenetic relationships, by restoration practitioners is recommended as a metric to allow consequences of the evolutionary patterns among species to be included in conservation planning. Increased accessibility of phylogenetic tools will allow the application of PD in restoration monitoring.
Drought responses by individual tree species are not often correlated with tree species diversity in European forests
Authors: Forrester David I. , Bonal Damien , Dawud Seid , Gessler Arthur , Granier André , Pollastrini Martina , Grossiord Charlotte 
Published: July 2016

Summary

Drought frequency and intensity are predicted to increase in many parts of the Northern Hemisphere and the effects of such changes on forest growth and tree mortality are already evident in many regions around the world. Mixed‐species forests and increasing tree species diversity have been put forward as important risk reduction and adaptation strategies in the face of climate change. However, little is known about whether the species interactions that occur in diverse forests will reduce drought susceptibility or water stress.

In this study, we focused on the effect of drought on individual tree species (n = 16) within six regions of Europe and assessed whether this response was related to tree species diversity and stand density, and whether community‐level responses resulted from many similar or contrasting species‐level responses. For each species in each plot, we calculated the increase in carbon isotope composition of latewood from a wet to a dry year (Δδ13C) as an estimate of its drought stress level.

When significant community‐level relationships occurred (three of six regions), there was only one species within the given community that showed a significant relationship (three of 25 species–region combinations), showing that information about a single species can be a poor indicator of the response of other species or the whole community.

There were many two‐species mixtures in which both species were less water‐stressed compared with their monocultures, but also many mixtures where both species were more stressed compared with their monocultures. Furthermore, a given species combination responded differently in different regions.

Synthesis and applications. Our study shows that drought stress may sometimes be reduced in mixed‐species forests, but this is not a general pattern, and even varies between sites for a given combination. The management or prediction of drought stress requires consideration of the physiological characteristics of the mixed species, and how this complements the water‐related climatic and edaphic features of the site, rather than species richness.
Stoichiometric modelling of assimilatory and dissimilatory biomass utilisation in a microbial community
Authors: Hunt Kristopher A. , Jennings Ryan deM. , Inskeep William P. , Carlson Ross P. 
Published: July 2016

SummaryAssimilatory and dissimilatory utilisation of autotroph biomass by heterotrophs is a fundamental mechanism for the transfer of nutrients and energy across trophic levels. Metagenome data from a tractable, thermoacidophilic microbial community in Yellowstone National Park was used to build an in silico model to study heterotrophic utilisation of autotroph biomass using elementary flux mode analysis and flux balance analysis. Assimilatory and dissimilatory biomass utilisation was investigated using 29 forms of biomass‐derived dissolved organic carbon (DOC) including individual monomer pools, individual macromolecular pools and aggregate biomass. The simulations identified ecologically competitive strategies for utilizing DOC under conditions of varying electron donor, electron acceptor or enzyme limitation. The simulated growth environment affected which form of DOC was the most competitive use of nutrients; for instance, oxygen limitation favoured utilisation of less reduced and fermentable DOC while carbon‐limited environments favoured more reduced DOC. Additionally, metabolism was studied considering two encompassing metabolic strategies: simultaneous versus sequential use of DOC. Results of this study bound the transfer of nutrients and energy through microbial food webs, providing a quantitative foundation relevant to most microbial ecosystems.
Enzymes involved in the anaerobic degradation of ortho‐phthalate by the nitrate‐reducing bacterium Azoarcus sp. strain PA01
Authors: Junghare Madan , Spiteller Dieter , Schink Bernhard 
Published: July 2016

SummaryThe pathway of anaerobic degradation of o‐phthalate was studied in the nitrate‐reducing bacterium Azoarcus sp. strain PA01. Differential two‐dimensional protein gel profiling allowed the identification of specifically induced proteins in o‐phthalate‐grown compared to benzoate‐grown cells. The genes encoding o‐phthalate‐induced proteins were found in a 9.9 kb gene cluster in the genome of Azoarcus sp. strain PA01. The o‐phthalate‐induced gene cluster codes for proteins homologous to a dicarboxylic acid transporter, putative CoA‐transferases and a UbiD‐like decarboxylase that were assigned to be specifically involved in the initial steps of anaerobic o‐phthalate degradation. We propose that o‐phthalate is first activated to o‐phthalyl‐CoA by a putative succinyl‐CoA‐dependent succinyl‐CoA:o‐phthalate CoA‐transferase, and o‐phthalyl‐CoA is subsequently decarboxylated to benzoyl‐CoA by a putative o‐phthalyl‐CoA decarboxylase. Results from in vitro enzyme assays with cell‐free extracts of o‐phthalate‐grown cells demonstrated the formation of o‐phthalyl‐CoA from o‐phthalate and succinyl‐CoA as CoA donor, and its subsequent decarboxylation to benzoyl‐CoA. The putative succinyl‐CoA:o‐phthalate CoA‐transferase showed high substrate specificity for o‐phthalate and did not accept isophthalate, terephthalate or 3‐fluoro‐o‐phthalate whereas the putative o‐phthalyl‐CoA decarboxylase converted fluoro‐o‐phthalyl‐CoA to fluoro‐benzoyl‐CoA. No decarboxylase activity was observed with isophthalyl‐CoA or terephthalyl‐CoA. Both enzyme activities were oxygen‐insensitive and inducible only after growth with o‐phthalate. Further degradation of benzoyl‐CoA proceeds analogous to the well‐established anaerobic benzoyl‐CoA degradation pathway of nitrate‐reducing bacteria.
Syntrophic associations from hypersaline soda lakes converting organic acids and alcohols to methane at extremely haloalkaline conditions
Authors: Sorokin Dimitry Y. , Abbas Ben , Geleijnse Mitchell , Kolganova Tatjana V. , Kleerebezem Robbert , van Loosdrecht Mark C. M. 
Published: July 2016

SummaryUntil now anaerobic oxidation of VFA at high salt‐pH has been demonstrated only at sulfate‐reducing conditions. Here, we present results of a microbiological investigation of anaerobic conversion of organic acids and alcohols at methanogenic conditions by syntrophic associations enriched from hypersaline soda lakes in Central Asia. Sediment incubation experiments showed active, albeit very slow, methane formation from acetate, propionate, butyrate and C2C4 alcohols at pH 10 and various levels of salinity. Enrichments of syntrophic associations using hydrogenotrophic members of the genus Methanocalculus from soda lakes as partners resulted in several highly enriched cultures converting acetate, propionate, butyrate, benzoate and EtOH to methane. Most syntrophs belonged to Firmicutes, while the propionate‐oxidizer formed a novel lineage within the family Syntrophobacteraceae in the Deltaproteobacteria. The acetate‐oxidizing syntroph was identified as ‘Ca. Syntrophonatronum acetioxidans’ previously found to oxidize acetate at sulfate‐reducing conditions up to salt‐saturating concentrations. Butyrate and a benzoate‐degrading syntrophs represent novel genus‐level lineages in Syntrophomonadales which are proposed as Candidatus taxons ‘Syntrophobaca’, ‘Syntrophocurvum’ and ‘Syntropholuna’. Overall, despite very slow growth, the results indicated the presence of a functionally competent syntrophic community in hypersaline soda lakes, capable of efficient oxidation of fermentation products to methane at extremely haloalkaline conditions.
Total Body Mass Estimation from Anthropometric Measurements in Modern Young Adult U.S. Populations with Healthy Body Fat Percentages (NHANES III)
Authors: Schaffer William C. 
Published: July 2016

AbstractThis study presents a method by which to estimate total body mass in modern young adult U.S. populations who self‐identified as non‐Hispanic U.S. White, non‐Hispanic U.S. Black, and Mexican American with anthropometric measurements from the Third National Health and Nutrition Examination Survey (NHANES III) 1988–1994 dataset (N = 2532). Correlations of stature and bi‐iliac breadth with total body mass were stronger among males (r = 0.717–0.774) than among females (r = 0.549–0.661), yet these results were more accurate assessments of total body mass than existing techniques. This study also examined additional anthropometric measurements to estimate total body mass using an information‐theoretic approach demonstrating that some error in the stature–bi‐iliac breadth method is attributed to a nonsupported model with multimodel inference. The limitations of the current total body mass technique are discussed as well as the need for future studies to validate the method.
Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling
Authors: Brewer Mark J. , O'Hara Robert B. , Anderson Barbara J. , Ohlemüller Ralf 
Published: July 2016

Summary

Ecologists often wish to describe mathematical relationships between response variables and climate covariates in spatial models of species distribution; these relationships are commonly termed climate envelopes. There are many situations when the functional form of the envelopes should be either unimodal or monotonic, but current practice tends towards the use of either low‐degree single‐variable spline curves fitted as part of a Generalised Additive Model (GAM) or piecewise linear forms in software such as maxent.
We argue that such curves are often inappropriate, as they: (i) can easily produce relationships which are ecologically implausible and (ii) frequently ignore interactions between multiple climate variables in a general regression context. We propose an novel alternative parametric form for climate envelopes that appeals to ecological plausibility and can encompass realistic features of species' presence/climate relationships on several variables simultaneously.
The proposed plateau climate envelope function is applied via a spatial Bayesian species distribution model to data on two European tree species to demonstrate the approach. For Fagus sylvatica, a complete climate envelope is estimable, but for Quercus coccifera, only a partial climate envelope can be estimated as the geographical extent of the data set does not cover the full environmental niche for the species. We show that such an approach is practical, produces climate envelopes with an ecologically meaningful form and furthermore allows the inclusion of information external to the data set being analysed.
We discuss the use of this new plateau climate envelope function in the context of ecological niche modelling and argue that in some instances ecological realism should be regarded as more important than the use of formal model comparison statistics.
Research trends and perspectives of male infertility: a bibliometric analysis of 20 years of scientific literature
Authors: Zhang Y. , Xiao F. , Lu S. , Song J. , Zhang C. , Li J. , Gu K. , Lan A. , Lv B. , Zhang R. , Mo F. , Jiang G. , Zhang X. , Yang X. 
Published: July 2016

SummaryTo carry out an in‐depth analysis of the scientific research on male infertility, we performed the first bibliometric analysis focusing on studies involving male infertility worldwide during the period 1995–2014. Analysis of 6357 articles in the field of male infertility showed a significant increasing trend in the number of publications over the period 1995–2014. Obstetrics and Gynecology was an important subject category and Multidisciplinary Sciences was the newest interest. Authors were mainly from Europe and USA, with researchers from Cleveland Clinic producing the most articles, and those from the Tel Aviv Sourasky Medical Center and the University of Utah having the highest‐quality articles. The USA contributed the most independent and international collaborative articles. The Cleveland Clinic and the University of Munster were the most productive institutions. The Cleveland Clinic and the University of Giessen had the most international collaboration publications. Harvard University had the most collaborators. The most common interests were pathogenesis and therapy, and new interests were hypogonadism, obesity, and cryopreservation. In conclusion, rapid development of the male infertility field was observed. Overall, collaborative and multidisciplinary science research has become more popular. The USA and its institutions play a dominant role, followed by European countries. Thanks to the common research focus worldwide, more insight into male fertility has been gained in the scientific literature over the past 20 years. [Correction added on September 21, 2016, after online publication: the term “institute” has been replaced by the term “institution” throughout the text.]
Pfannenstiel laparoendoscopic reduced‐port radical nephrectomy
Authors: Yamasaki Mutsushi , Shin Toshitaka , Sato Ryuta , Hirai Kenichi , Kan Tomoko , Fujinami Hiroyuki , Mori Kenichi , Sumino Yasuhiro , Nomura Takeo , Sato Fuminori , Masuda Hitoshi , Yonese Junji , Mimata Hiromitsu 
Published: July 2016

AbstractIntroductionWe previously reported cases of laparoendoscopic single‐site nephrectomy performed through an umbilical or pararectal incision. To improve cosmesis and operability, we performed three Pfannenstiel laparoendoscopic reduced‐port nephrectomies.Materials and Surgical TechniqueIn the first case, a GelPOINT access was placed through a 2‐cm umbilical incision, and two additional 3‐mm trocars were inserted. The specimen was extracted through a 4‐cm Pfannenstiel incision. In the second and third cases, a GelPOINT access was placed through a 5‐cm Pfannenstiel incision, and two additional 3‐mm trocars were inserted. The specimens were extracted without additional skin incisions. In all cases, the endoscope and vessel‐sealing device were inserted through the GelPOINT access. We used 3‐mm scissors, dissecting forceps, and bipolar forceps.DiscussionThe operating time and estimated blood loss were 228, 280, and 155 min and 10, 410, and 5 mL, respectively. There were no intraoperative or postoperative complications. The 3‐mm forceps showed similar efficacy as the conventional 5‐mm forceps. Therefore, a Pfannenstiel reduced‐port nephrectomy using 3‐mm working trocars is a safe and feasible procedure with good cosmesis.
Risk factors and a clinical prediction model for low maternal thyroid function during early pregnancy: two population‐based prospective cohort studies
Authors: Korevaar Tim I.M. , Nieboer Daan , Bisschop Peter H.L.T. , Goddijn Mariette , Medici Marco , Chaker Layal , de Rijke Yolanda B. , Jaddoe Vincent W.V. , Visser Theo J. , Steyerberg Ewout W. , Tiemeier Henning , Vrijkotte Tanja G. , Peeters Robin P. 
Published: July 2016

SummaryBackgroundLow maternal thyroid function during early pregnancy is associated with various adverse outcomes including impaired neurocognitive development of the offspring, premature delivery and abnormal birthweight.AimTo aid doctors in the risk assessment of thyroid dysfunction during pregnancy, we set out to investigate clinical risk factors and derive a prediction model based on easily obtainable clinical variables.MethodsIn total, 9767 women during early pregnancy (≤18 week) were selected from two population‐based prospective cohorts: the Generation R Study (N = 5985) and the ABCD study (N = 3782). We aimed to investigate the association of easily obtainable clinical subject characteristics such as maternal age, BMI, smoking status, ethnicity, parity and gestational age at blood sampling with the risk of low free thyroxine (FT4) and elevated thyroid stimulating hormone (TSH), determined according to the 2·5th–97·5th reference range in TPOAb negative women.ResultsBMI, nonsmoking and ethnicity were risk factors for elevated TSH levels; however, the discriminative ability was poor (range c‐statistic of 0·57–0·60). Sensitivity analysis showed that addition of TPOAbs to the model yielded a c‐statistic of 0·73–0·75. Maternal age, BMI, smoking, parity and gestational age at blood sampling were risk factors for low FT4, which taken together provided adequate discrimination (range c‐statistic of 0·72–0·76).ConclusionsElevated TSH levels depend predominantly on TPOAb levels, and prediction of elevated TSH levels is not possible with clinical characteristics only. In contrast, the validated clinical prediction model for FT4 had high discriminative value to assess the likelihood of low FT4 levels.
FGFs: crucial factors that regulate tumour initiation and progression
Authors: Jing Qian , Wang Yuanyuan , Liu Hao , Deng Xiaowei , Jiang Lin , Liu Rui , Song Haixing , Li Jingyi 
Published: July 2016

AbstractFibroblast growth factors (FGFs) are crucial signalling molecules involved in normal cell growth, differentiation and proliferation. Over the past few decades, a large body of research has illustrated effects of individual FGFs on tumour initiation and progression. Tumour development is commonly accompanied with generation of new blood and lymph vessels, which support enhanced cell proliferation. Moreover, acquisition of tumour cells of the epithelial–mesenchymal transition (EMT) phenotype, enhances tumour cell migration and invasion potentials, crucial steps in tumour metastasis. This review summarizes recent findings concerning roles of FGFs in angiogenesis, lymphangiogenesis and EMT.
Botulinum neurotoxin treatment in children with cerebral palsy: validation of a needle placement protocol using passive muscle stretching and relaxing
Authors: Warnink‐Kavelaars Jessica , Vermeulen R Jeroen , Buizer Annemieke I , Becher Jules G 
Published: July 2016

AimTo validate a detailed intramuscular needle placement protocol using passive muscle stretching and relaxing for botulinum neurotoxin type A (BoNT‐A) treatment in the lower extremity of children with spastic cerebral palsy (CP), with verification by electrical stimulation.MethodA prospective observational study was performed in 75 children with spastic CP who received regular BoNT‐A treatment under general anaesthesia (52 males, 23 females; mean age 8y 9mo, SD 3y 7mo, range 4–18y; mean body mass index 16.2, SD 3.7, range 7.7–26.7). A total of 1084 intramuscular needle placements using passive muscle stretching and relaxing were verified by electrical stimulation. Primary outcome was the positive predictive value.ResultsIntramuscular needle placement in the muscles adductor brevis, adductor longus, gracilis, semimembranosus, semitendinosus, biceps femoris, rectus femoris, and lateral and medial heads of the gastrocnemius and soleus had a positive predictive value ranging from 85.7% to 100% (95% confidence interval ranging from 71.5–89.9% to 91.4–100%).InterpretationThis validated detailed protocol for intramuscular needle placement using passive muscle stretching and relaxing for BoNT‐A treatment in the lower extremity of children with spastic CP is reliable and has a high positive predictive value.
Oviposition choice and larval performance of Neomusotima conspurcatalis on leaflet types of the invasive fern, Lygodium microphyllum
Authors: Smith Melissa C. , Lake Ellen C. , Wheeler Gregory S. 
Published: July 2016

AbstractLygodium microphyllum (Cavanilles) R Brown (Lygodiaceae), Old World climbing fern, invades wildlands in central and southern Florida, USA, and causes considerable habitat disturbance. Efforts to develop an effective biological control strategy have focused on several folivorous insects and a leaf‐galling mite from southeast Asia and Australia. Neomusotima conspurcatalis Warren (Lepidoptera: Crambidae) is a foliage‐feeding moth that specializes on Lygodium species. First released in 2008, N. conspurcatalis successfully established in Florida and is dispersing throughout the L. microphyllum‐invaded range. We investigated whether N. conspurcatalis display any preference (oviposition or larval feeding) between two leaflet morphologies, i.e., fertile spore‐producing vs. sterile leaflets. Furthermore, we examined whether oviposition and no‐choice diets on either fern leaflet type conferred any possible selective advantages (e.g., weight, emergence success) to the offspring. Finally, we analyzed leaf nitrogen and carbon content and leaf volatiles to gauge differences between the leaflet types. In choice and no‐choice scenarios, larvae consume approximately the same amount of leaf area and display no preference between fertile and sterile leaflets. However, females deposited significantly more eggs on fertile than on sterile leaflets. Oviposition choice had no effect on larval development times, pupal weights, or successful eclosure. Nitrogen and carbon content did not differ between fertile and sterile samples, but sterile leaflets contain more 1‐octen‐3‐ol, which may act as an herbivory deterrent. The propagule attack imposed by N. conspurcatalis feeding on fertile leaflets is unlikely to provide adequate control, but could be beneficial as part of a suite of biological control agents and other control methods.