bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
Authors: Deiner Kristy , Bik Holly M. , Mächler Elvira , Seymour Mathew , Lacoursière‐Roussel Anaïs , Altermatt Florian , Creer Simon , Bista Iliana , Lodge David M. , de Vere Natasha , Pfrender Michael E. , Bernatchez Louis 
Published: September 2017

AbstractThe genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
Effects of zoochory on the spatial genetic structure of plant populations
Authors: Gelmi‐Candusso Tiziana A. , Heymann Eckhard W. , Heer Katrin 
Published: September 2017

AbstractSpatial genetic structure (SGS) of plants results from the nonrandom distribution of related individuals.SGSprovides information on gene flow and spatial patterns of genetic diversity within populations. Seed dispersal creates the spatial template for plant distribution. Thus, in zoochorous plants, dispersal mode and disperser behaviour might have a strong impact onSGS. However, many studies only report the taxonomic group of seed dispersers, without further details. The recent increase in studies onSGSprovides the opportunity to review findings and test for the influence of dispersal mode, taxonomic affiliation of dispersers and their behaviour. We compared the proportions of studies withSGSamong groups and tested for differences in strength ofSGSusingSpstatistics. The presence ofSGSdiffered among taxonomic groups, with reduced presence in plants dispersed by birds. Strength ofSGSwas instead significantly influenced by the behaviour of seed dispersal vectors, with higherSGSin plant species dispersed by animals with behavioural traits that result in short seed dispersal distances. We observed high variance in the strength ofSGSin plants dispersed by animals that actively or passively accumulate seeds. Additionally, we foundSGSwas also affected by pollination and marker type used. Our study highlights the importance of vector behaviour onSGSeven in the presence of variance created by other factors. Thus, more detailed information on the behaviour of seed dispersers would contribute to better understand which factors shape the spatial scale of gene flow in animal‐dispersed plant species.
Mutual independence of alkaline‐ and calcium‐mediated signalling in Aspergillus fumigatus refutes the existence of a conserved druggable signalling nexus
Authors: Loss Omar , Bertuzzi Margherita , Yan Yu , Fedorova Natalie , McCann Bethany L. , Armstrong‐James Darius , Espeso Eduardo A. , Read Nick D. , Nierman William C. , Bignell Elaine M. 
Published: September 2017

SummaryFunctional coupling of calcium‐ and alkaline responsive signalling occurs in multiple fungi to afford efficient cation homeostasis. Host microenvironments exert alkaline stress and potentially toxic concentrations of Ca2+, such that highly conserved regulators of both calcium‐ (Crz) and pH‐ (PacC/Rim101) responsive signalling are crucial for fungal pathogenicity. Drugs targeting calcineurin are potent antifungal agents but also perturb human immunity thereby negating their use as anti‐infectives, abrogation of alkaline signalling has, therefore, been postulated as an adjunctive antifungal strategy. We examined the interdependency of pH‐ and calcium‐mediated signalling in Aspergillus fumigatus and found that calcium chelation severely impedes hyphal growth indicating a critical requirement for this ion independently of ambient pH. Transcriptomic responses to alkaline pH or calcium excess exhibited minimal similarity. Mutants lacking calcineurin, or its client CrzA, displayed normal alkaline tolerance and nuclear translocation of CrzA was unaffected by ambient pH. Expression of a highly conserved, alkaline‐regulated, sodium ATPase was tolerant of genetic or chemical perturbations of calcium‐mediated signalling, but abolished in null mutants of the pH‐responsive transcription factor PacC, and PacC proteolytic processing occurred normally during calcium excess. Taken together our data demonstrate that in A. fumigatus the regulatory hierarchy governing alkaline tolerance circumvents calcineurin signalling.
The ribokinases of Arabidopsis thaliana and Saccharomyces cerevisiae are required for ribose recycling from nucleotide catabolism, which in plants is not essential to survive prolonged dark stress
Authors: Schroeder Rebekka Y. , Zhu Anting , Eubel Holger , Dahncke Kathleen , Witte Claus‐Peter 
Published: September 2017

Summary

Nucleotide catabolism in Arabidopsis thaliana and Saccharomyces cerevisiae leads to the release of ribose, which requires phosphorylation to ribose‐5‐phosphate mediated by ribokinase (RBSK). We aimed to characterize RBSK in plants and yeast, to quantify the contribution of plant nucleotide catabolism to the ribose pool, and to investigate whether ribose carbon contributes to dark stress survival of plants.

We performed a phylogenetic analysis and determined the kinetic constants of plant‐expressed Arabidopsis and yeast RBSKs. Using mass spectrometry, several metabolites were quantified in AtRBSK mutants and double mutants with genes of nucleoside catabolism. Additionally, the dark stress performance of several nucleotide metabolism mutants and rbsk was compared.

The plant PfkB family of sugar kinases forms nine major clades likely representing distinct biochemical functions, one of them RBSK. Nucleotide catabolism is the dominant ribose source in plant metabolism and is highly induced by dark stress. However, rbsk cannot be discerned from the wild type in dark stress. Interestingly, the accumulation of guanosine in a guanosine deaminase mutant strongly enhances dark stress symptoms.

Although nucleotide catabolism contributes to carbon mobilization upon darkness and is the dominant source of ribose, the contribution appears to be of minor importance for dark stress survival.
Effects of pre‐surgical nasoalveolar moulding on maxillary arch and nasal form in unilateral cleft lip and palate before lip surgery
Authors: Fuchigami T. , Kimura N. , Kibe T. , Tezuka M. , Amir M. S. , Suga H. , Takemoto Y. , Hashiguchi M. , Maeda‐Iino A. , Nakamura N. 
Published: September 2017

Structured AbstractObjectivesTo investigate the effects of pre‐surgical nasoalveolar moulding (PNAM) on the maxillary arch and nasal form in patients with unilateral cleft lip and palate (UCLP).Setting and Sample PopulationThis is a retrospective case series study. The subjects were infants with complete UCLP who were treated with PNAM (n = 18) at Kagoshima University Medical and Dental Hospital (Japan) between 2006 and 2013.Material and MethodsMaxillary dental casts and facial photographs were taken at the time of the first visit and immediately prior to lip surgery to evaluate the maxillary arch and nasal form changes. The dental casts were scanned with a laser scanner, and changes in the 3‐Dimensional coordinates of anatomical landmarks and alveolar cleft width were analysed. Moreover, we investigated the correlation between the changes in the maxillary alveolar arch and nasal form.ResultsRegarding the maxillary alveolar arch form, the anterior points of the major segment had moved significantly to the cleft side just prior to the time of lip repair, and the alveolar cleft width was significantly decreased. For nasal form, the inclination and displacement of the columella were significantly improved. The improvement of columella inclination was moderately correlated with the posterior movement of the anterior points of the major segment.ConclusionsThese findings indicate that PNAM for infants with UCLP enhanced symmetry in the maxillary alveolar arch and nasolabial form. In addition, the posterior movement of the anterior points of the maxillary alveolar arch was correlated with the improvement of columella deformation.
Low‐gluten, nontransgenic wheat engineered with CRISPR/Cas9
Authors: Sánchez‐León Susana , Gil‐Humanes Javier , Ozuna Carmen V. , Giménez María J. , Sousa Carolina , Voytas Daniel F. , Barro Francisco 
Published: September 2017

SummaryCoeliac disease is an autoimmune disorder triggered in genetically predisposed individuals by the ingestion of gluten proteins from wheat, barley and rye. The α‐gliadin gene family of wheat contains four highly stimulatory peptides, of which the 33‐mer is the main immunodominant peptide in patients with coeliac. We designed two sgRNAs to target a conserved region adjacent to the coding sequence for the 33‐mer in the α‐gliadin genes. Twenty‐one mutant lines were generated, all showing strong reduction in α‐gliadins. Up to 35 different genes were mutated in one of the lines of the 45 different genes identified in the wild type, while immunoreactivity was reduced by 85%. Transgene‐free lines were identified, and no off‐target mutations have been detected in any of the potential targets. The low‐gluten, transgene‐free wheat lines described here could be used to produce low‐gluten foodstuff and serve as source material to introgress this trait into elite wheat varieties.
Generalized Additive Models with Principal Component Analysis: An Application to Time Series of Respiratory Disease and Air Pollution Data
Authors: Souza Juliana B. , Reisen Valdério A. , Franco Glaura C. , Ispány Márton , Bondon Pascal , Santos Jane Meri 
Published: September 2017

SummaryEnvironmental epidemiological studies of the health effects of air pollution frequently utilize the generalized additive model (GAM) as the standard statistical methodology, considering the ambient air pollutants as explanatory covariates. Although exposure to air pollutants is multi-dimensional, the majority of these studies consider only a single pollutant as a covariate in the GAM model. This model restriction may be because the pollutant variables do not only have serial dependence but also interdependence between themselves. In an attempt to convey a more realistic model, we propose here the hybrid generalized additive model–principal component analysis–vector auto-regressive (GAM–PCA–VAR) model, which is a combination of PCA and GAMs along with a VAR process. The PCA is used to eliminate the multicollinearity between the pollutants whereas the VAR model is used to handle the serial correlation of the data to produce white noise processes as covariates in the GAM. Some theoretical and simulation results of the methodology proposed are discussed, with special attention to the effect of time correlation of the covariates on the PCA and, consequently, on the estimates of the parameters in the GAM and on the relative risk, which is a commonly used statistical quantity to measure the effect of the covariates, especially the pollutants, on population health. As a main motivation to the methodology, a real data set is analysed with the aim of quantifying the association between respiratory disease and air pollution concentrations, especially particulate matter PM10, sulphur dioxide, nitrogen dioxide, carbon monoxide and ozone. The empirical results show that the GAM–PCA–VAR model can remove the auto-correlations from the principal components. In addition, this method produces estimates of the relative risk, for each pollutant, which are not affected by the serial correlation in the data. This, in general, leads to more pronounced values of the estimated risk compared with the standard GAM model, indicating, for this study, an increase of almost 5.4% in the risk of PM10, which is one of the most important pollutants which is usually associated with adverse effects on human health.
How Important Are Scale Effects for Growth When Knowledge Is a Public Good?
Authors: Sánchez‐Losada Fernando 
Published: September 2017

AbstractIn this paper, by proposing an R&D accumulation law for an economy with an expanding number of firms, I seek to reconcile the following three facts: the positive relationship between the fraction of income allocated to R&D expenditure and growth; the positive relationship between the number of firms and total factor productivity growth; and knowledge as a non‐rival and non‐excludable good. There are scale effects because of the public nature of knowledge, but the economy also grows in the absence of population growth. I find that population growth explains one‐fifth of market income growth but only one‐sixteenth of efficient income growth.
Pitfalls in accelerometer‐based measurement of physical activity: The presence of reactivity in an adult population
Authors: Baumann S. , Groß S. , Voigt L. , Ullrich A. , Weymar F. , Schwaneberg T. , Dörr M. , Meyer C. , John U. , Ulbricht S. 
Published: September 2017

When a behavior is monitored, it is likely to change, even if no change may be intended. This phenomenon is known as measurement reactivity. We investigated systematic changes in accelerometer‐based measures over the days of monitoring as an indicator of measurement reactivity in an adult population. One hundred seventy‐one participants from the general population (65% women; mean age = 55 years, range: 42‐65 years) wore accelerometers for 7 consecutive days to measure sedentary behavior and physical activity (PA). Latent growth models were used (a) to investigate changes in accelerometer wear time over the measurement days and (b) to identify measurement reactivity indicated by systematic changes in sedentary time (ST), light physical activity (LPA), and moderate‐to‐vigorous physical activity (MVPA). Over the measurement days, participants reduced accelerometer wear time by trend (rate of change [b] = −4.7 min/d, P = .051, Cohen's d = .38), increased ST (b = 2.4 min/d, P = .018, d = .39), and reduced LPA (b = −2.4 min/d, P = .015, d = .38). Participants did not significantly reduce MVPA (P = .537). Our data indicated that accelerometry might generate reactivity. Small effects on ST and LPA were found. Thus, the validity of accelerometer‐based data on ST and LPA may be compromised. Systematic changes observed in accelerometer wear time may further bias accelerometer‐based measures. MVPA seems to be less altered due to the presence of an accelerometer.
Bridging the Implementation Gap in Poor Areas: A Study of How Municipal Socio‐economic Characteristics Impact Intergovernmental Policy Implementation
Authors: Galvani Flávia 
Published: September 2017

AbstractThis article examines the relationship between local socio‐economic characteristics and implementation performance by analyzing the performance of Brazilian municipalities implementing the Bolsa Família Program, the largest conditional cash transfer programme in the world. Counterintuitively, poor municipalities were found to outperform wealthy ones. Analysis of the interactions between local socio‐economic characteristics and municipal administrative capacity, willingness and intergovernmental relations help to explain why this was the case.
Early Cretaceous exhumation of the Qiangtang Terrane during collision with the Lhasa Terrane, Central Tibet
Authors: Zhao Zhongbao , Bons Paul D. , Stübner Konstanze , Wang Gen‐Hou , Ehlers Todd A. 
Published: September 2017

AbstractThe timing of the closure of the Bangong Ocean between the Lhasa and South Qiangtang Terranes in central Tibet and the resulting crustal thickening are still under debate. We integrate published apatite fission track and (U–Th)/He thermochronometer data with new zircon (U–Th)/He ages from eight samples and with structural profiles to document that the South Qiangtang Terrane experienced slow exhumation between 200 and 150 Ma, associated with the opening of the Bangong Ocean. Accelerated exhumation (around 0.2–0.3 mm/a) of the South Qiangtang Terrane was initiated at around 150 Ma. This exhumation event is interpreted to reflect collision between the Lhasa and South Qiangtang Terranes after closure of the Bangong Ocean, associated with crustal thickening via thick‐skinned folding and thrusting within the South Qiangtang Terrane. The amalgamation of the Lhasa and South Qiangtang Terranes recorded here may represent the first stage of crustal thickening in the central Tibetan Plateau.
Identification of occult active infection using PET‐CT in a combined liver‐kidney transplant candidate
Authors: Al Shakarchi Julien , Neil Desley , Lipkin Graham , Elsharkawy Ahmed , Inston Nicholas 
Published: September 2017

AbstractThis case describes a patient being considered for combined liver‐kidney transplantation for Caroli's disease with a failed renal transplant. A chronic septic focus could not be located with standard imaging techniques, such as ultrasonography and computed tomography. This case report highlights the observation that a retained non‐functioning transplant can be the cause of fever of unknown origin and PET‐CT can be useful in diagnosing these challenging cases.
Barriers to listing for HIV‐infected patients being evaluated for kidney transplantation
Authors: Lee Dong Heun , Boyle Suzanne M. , Malat Gregory E. , Kern Christopher , Milrod Charles , DeBellis Shannon , Harhay Meera N. , Ranganna Karthik , Guy Stephen , Talluri Sindhura , Bias Tiffany , Doyle Alden 
Published: September 2017

AbstractHuman immunodeficiency virus (HIV)‐infected patients have excellent outcomes following kidney transplantation (KT) but still might face barriers in the evaluation and listing process. The aim of this study was to characterize the patient population, referral patterns, and outcomes of HIV‐infected patients who present for KT evaluation. We performed a single‐center retrospective cohort study of HIV‐infected patients who were evaluated for KT. The primary outcome was time to determination of eligibility for KT. Between 2011 and 2015, 105 HIV‐infected patients were evaluated for KT. Of the 105 patients, 73 were listed for transplantation by the end of the study period. For those who were deemed ineligible, the most common reasons cited were active substance abuse (n = 7, 22%) and failure to complete the full transplant evaluation (n = 7, 22%). Our cohort demonstrated a higher proportion of HIV‐infected patients eligible for KT than in previous studies, likely secondary to advances in HIV management. Among those who were denied access to transplantation, we identified that many were unable to complete the evaluation process, and that active substance abuse was common. Future prospective studies should examine reasons and potential interventions for the lack of follow‐through and drug use we observed in this population.
Valganciclovir (VGCV) followed by cytomegalovirus (CMV) hyperimmune globulin compared to VGCV for 200 days in abdominal organ transplant recipients at high risk for CMV infection: A prospective, randomized pilot study
Authors: Fleming James N. , Taber David J. , Weimert Nicole A. , Nadig Satish , McGillicuddy John W. , Bratton Charles F. , Baliga Prabhakar K. , Chavin Kenneth D. 
Published: September 2017

AbstractBackgroundWith the advent of effective antivirals against cytomegalovirus (CMV), use of CMV hyperimmune globulin (HIG) has decreased. Although antiviral prophylaxis in patients at high risk for CMV is effective, many patients still have late infection, never developing antibodies sufficient to achieve immunity. Utilizing a combination of antiviral and CMV HIG may allow patients to achieve immunity and decrease late CMV infections.MethodsThis was a prospective randomized, open‐label, pilot study comparing valganciclovir (VGCV) prophylaxis for 200 days vs VGCV for 100 days followed by CMV HIG in abdominal transplant recipients at high risk for CMV. The primary outcome was a comparison of late CMV disease.ResultsForty patients were randomized to VGCV for 200 days (n = 20) or VGCV for 100 days followed by 3 doses of monthly CMV HIG (n = 20). Numerically, more overall CMV infections occurred in the CMV HIG group (45 vs 20%, P = .09). No differences in overall CMV infections or late CMV disease were seen between groups (20% vs 15%, P = 1.00 and 0 vs 0, P = 1.00). All CMV disease occurred within 200 days, with 63% occurring while patients were on VGCV. No differences were found in toxicities, graft function, or rejection between groups. Patients with CMV infection at any time had a higher body weight than those who did not have an infection (82 vs 95 kg, P = .049).ConclusionUse of CMV HIG sequentially with prophylaxis may be an effective and affordable prophylactic regimen in abdominal transplant recipients at high risk for CMV, and warrants larger prospective study. Increased monitoring for patients with obesity may be warranted.
Immunomodulatory effect of cryopreserved platelets: altered BDCA3+ dendritic cell maturation and activation in vitro
Authors: Ki Katrina K. , Johnson Lacey , Faddy Helen M. , Flower Robert L. , Marks Denese C. , Dean Melinda M. 
Published: September 2017

BACKGROUNDCryopreservation of platelets (PLTs) is useful in remote areas to overcome logistic problems associated with supply and can extend the shelf life to 2 years. During cryopreservation, properties of PLTs are modified. Whether changes in the cryopreserved PLT (CPP) product are associated with modulation of recipients’ immune function is unknown. We aimed to characterize the immune profile of myeloid dendritic cells (mDCs) and the specialized blood DC antigen (BDCA)3+ subset after exposure to CPPs.STUDY DESIGN AND METHODSUsing an in vitro whole blood model of transfusion, the effect of CPPs on mDC and BDCA3+ DC surface antigen expression and inflammatory mediator production was examined using flow cytometry. In parallel, polyinosinic:polycytidylic acid (poly(I:C)) or lipopolysaccharide (LPS) was utilized to model processes activated in viral or bacterial infection, respectively.RESULTSCryopreserved PLTs had minimal impact on mDC responses but significantly modulated BDCA3+ DC responses in vitro. Exposure to CPPs alone up regulated BDCA3+ DC CD86 expression and suppressed interleukin (IL)‐8, tumor necrosis factor (TNF)‐α, and interferon‐γ inducible protein (IP)‐10 production. In both models of infection‐related processes, exposure to CPPs down regulated BDCA3+ DC expression of CD40, CD80, and CD83 and suppressed BDCA3+ DC production of IL‐8, IL‐12, and TNF‐α. CPPs suppressed CD86 expression in the presence of LPS and IP‐10 and IL‐6 production with poly(I:C).CONCLUSIONCryopreserved PLTs may be immunosuppressive, and this effect is more evident when processes associated with infection are concurrently activated, especially for BDCA3+ DCs. This suggests that transfusion of CPPs in patients with infection may result in impaired BDCA3+ DC responses.