bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fossils know it best: using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Myomorpha: Muroidea: Muridae)
Authors: Aghová Tatiana , Kimura Yuri , Bryja Josef , Dobigny Gauthier , Granjon Laurent , Kergoat Gael J. 
Published: September 2017

AbstractMurid rodents (Rodentia: Myomorpha: Muroidea: Muridae) represent the most diverse and abundant mammalian group. In this study, we reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 160 species representing 82 distinct murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae, and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of multiple fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 23.0-16.0 million years ago (Ma), and that most major lineages (i.e. tribes) have started diversifyingca.10 Ma. Historical biogeography analyses support the Paleotropical origin for the family, with an initial internal split (vicariance event) followed by subsequent migrations between Afrotropical and Indomalayan lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions, mostly from the Indomalaya. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.
Dose-response surface fits to drought and nitrogen limitation applied together allow mapping of loci that exhibit nonlinear responses
Authors: Chang Megan M. , Nail Danielle Allery , Kazic Toni , Simmons Susan J. , Stapleton Ann E. 
Published: September 2017

ABSTRACTCrop improvement must accelerate to feed an increasing human population in the face of environmental changes. Breeding programs can include anticipated climatic changes and genetic architecture to optimize improvement strategies. We analyzed the genetic architecture underlying the response of Zea mays to combinations of water and nitrogen stresses. Recombinant inbreds were subjected to nine combinations of the two stresses using an optimized response surface design, and their growth was measured. Three-dimensional dose response surfaces were fit globally and to each polymorphic allele to determine which genetic markers were associated with different response surfaces. Three quantitative trait loci that produced nonlinear surfaces were mapped. Alleles that performed better in combinations of mid-range stresses were typically not the alleles that performed best under combinations of extreme stresses. To develop physiologically relevant models for future genetic analyses, we modeled the network that explains the response surfaces. The network contains two components, an elliptical paraboloid and a plane, that each combine the nitrogen and water inputs. The relative weighting of the two components and the inputs is governed by five parameters. We estimated parameter values for the smoothed surfaces from the experimental lines using a set of points that covered the most distinctive regions of the three-dimensional surfaces. Surfaces computed using these values reproduced the smoothed experimental surfaces well, especially in the neighborhood of the peaks, as judged by three different criteria. The parameters exaggerated the amplitudes of the simulated surfaces. Experiments using single stresses could misestimate responses to their combinations and disguise loci that respond nonlinearly. The three-dimensional shape evaluation strategy used here more thoroughly compares nonlinear, nonplanar responses. We encourage the application of our findings and methods to experiments that mix crop protection measures, stresses, or both, on elite and landrace germplasm.
Macroecology suggests cancer-causing papillomaviruses form non-neutral communities
Authors: Félez-Sánchez Marta , Murall Carmen Lía , Bravo Ignacio G. 
Published: September 2017

ABSTRACTChronic infection by oncogenic Human papillomaviruses (HPVs) leads to cancers. Public health interventions, such as cancer screening and mass vaccination, radically change the ecological conditions encountered by circulating viruses. It is currently unclear how HPVs communities may respond to these environmental changes, because little is known about their ecology. Predicting the impact on viral diversity by the introduction of HPV vaccines requires answering the unresolved question of how HPVs interact. Although it is commonly believed that they do not interact (neutral theory), there are suggestions that HPV types may compete for resources or via the immune response (niche-based or non-neutral theory). Here, we applied for the first time established biodiversity measures and methods to epidemiological data in order to assess whether niche-partitioning or neutral processes are shaping HPV diversity patterns at the population level. We find that as infections progress toward cancer, HPVs communities become more uneven and a few HPVs play a stronger dominance role. By fitting species abundance distributions, we found that neutral models were always out-performed by non-neutral distributions, both in asymptomatic infections and in cancers. Our results suggest that temporally moving from a more even to a less even community implies an increase in competition, probably due to environmental changes linked to infection progression. More ecological thinking will be required to understand present-day interactions and to anticipate the future of the long lasting interactions between HPVs and humans.SIGNIFICANCE STATEMENTHuman papillomaviruses (HPVs) are very diverse. Infections by HPVs are very common and chronic infections may lead to cancers. The more oncogenic HPVs are now targetted by effective vaccines, and this has raised the question of whether there may be a viral replacement if these dominant types were removed. This is a medical version of a classical ecological controversy, namely how much biodiversity distributions and community dynamics are explained by neutral theory plays out across ecosystems. For HPVs, epidemiologic studies before and after the vaccination have led to the widespread belief that these viruses do not interact. Here, we apply different methods developed in macroecology to the best available epidemiologic data to address this issue. Consistently, we find that HPVs form non-neutral communities. Instead, competitive niche-partitioning process and dominance explain best HPVs communities. We also find that the vaccine might not change such competitive niche processes. Beyond clinical implications, this garners support that niche processes often best explain biodiversity patterns, even in human viral communities.
Data-driven Topological Filtering based on Orthogonal Minimal Spanning Trees: Application to Multi-Group MEG Resting-State Connectivity
Authors: Dimitriadis Stavros I. , Antonakakis Marios , Simos Panagiotis , Fletcher Jack M. , Papanicolau Andrew C. 
Published: September 2017

AbstractIn the present study a novel data-driven topological filtering technique is introduced to derive the backbone of functional brain networks relying on orthogonal minimal spanning trees (OMST). The method aims to identify the essential functional connections to ensure optimal information flow via the objective criterion of global efficiency minus the cost of surviving connections. The OMST technique was applied to multichannel, resting-state neuromagnetic recordings from four groups of participants: healthy adults (n=50), adults who have suffered mild traumatic brain injury (n=30), typically developing children (n=27), and reading-disabled children (n=25). Weighted interactions between network nodes (sensors) were computed using an integrated approach of dominant intrinsic coupling modes based on two alternative metrics (symbolic mutual information and phase lag index), resulting in excellent discrimination of individual cases according to their group membership. Classification results using OMST-derived functional networks were clearly superior to results using either relative power spectrum features or functional networks derived through the conventional minimal spanning trees algorithm.
Microinjection to deliver protein, mRNA, and DNA into zygotes of the cnidarian endosymbiosis modelAiptasiasp.
Authors: Jones Victor A. S. , Bucher Madeline , Hambleton Elizabeth A. , Guse Annika 
Published: September 2017

AbstractReef-building corals depend on an intracellular symbiosis with photosynthetic dinoflagellates for their survival in nutrient-poor oceans. Symbionts are phagocytosed by coral larvae from the environment and transfer essential nutrients to their hosts.Aiptasia, a small tropical marine sea anemone, is emerging as a tractable model system for coral symbiosis; however, to date functional tools and genetic transformation are lacking. Here we have established an efficient workflow to collectAiptasiaeggs forin vitrofertilization and microinjection as the basis for experimental manipulations in the developing embryo and larvae. We demonstrate that protein, mRNA, and DNA can successfully be injected into liveAiptasiazygotes to label actin with recombinant Lifeact-eGFP protein; to label nuclei and cell membranes with NLS-eGFP and farnesylated mCherry translated from injected mRNA; and to transiently drive transgene expression from anAiptasia-specific promoter, respectively, in embryos and larvae. These proof-of-concept approaches pave the way for future functional studies of development and symbiosis establishment inAiptasia, a powerful model to unravel the molecular mechanisms underlying intracellular coral-algal symbiosis.Summary StatementToolkit extension: development of microinjection for cellular labelling, expression of exogenous genes and live imaging inAiptasia, an emerging model for intracellular coral-algal symbiosis.
No major flaws in “Identification of individuals by trait prediction using whole-genome sequencing data”
Authors: Lippert Christoph , Sabatini Riccardo , Maher M. Cyrus , Kang Eun Yong , Lee Seunghak , Arikan Okan , Harley Alena , Bernal Axel , Garst Peter , Lavrenko Victor , Yocum Ken , Wong Theodore M. , Zhu Mingfu , Yang Wen-Yun , Chang Chris , Hicks Barry , Ramakrishnan Smriti , Tang Haibao , Xie Chao , Brewerton Suzanne , Turpaz Yaron , Telenti Amalio , Roby Rhonda K. , Och Franz , Venter J. Craig 
Published: September 2017

AbstractIn a recently published PNAS article, we studied the identifiability of genomic samples using machine learning methods [Lippert et al., 2017]. In a response, Erlich [2017] argued that our work contained major flaws. The main technical critique of Erlich [2017] builds on a simulation experiment that shows that our proposed algorithm, which uses only a genomic sample for identification, performed no better than a strategy that uses demographic variables. Below, we show why this comparison is misleading and provide a detailed discussion of the key critical points in our analyses that have been brought up in Erlich [2017] and in the media. Further, not only faces may be derived from DNA, but a wide range of phenotypes and demographic variables. In this light, the main contribution of Lippert et al. [2017] is an algorithm that identifies genomes of individuals by combining multiple DNA-based predictive models for a myriad of traits.
The impact of personal resources on turnover intention
Authors: Kim Woocheol , Hyun Young Sup 
Published: September 2017

PurposeThis paper aims to investigate mediating effects of employees’ work engagement in the relationships between their personal resources (i.e. self-efficacy, organizational-based self-esteem and optimism) and turnover intention within Korean organizations.Design/methodology/approachA total of 571 survey responses collected from Korean organizations were utilized and analyzed to test the proposed research hypotheses by using structural equation modeling.FindingsThe results showed that all of personal resources had a positive impact on work engagement and work engagement had a negative impact on turnover intention. The results also revealed that although both organizational-based self-esteem and optimism had a negative impact on turnover intention, self-efficacy had an impact on turnover intention with the opposite way. In addition, work engagement mediated the relationships among self-efficacy, organizational-based self-esteem, optimism and turnover intention.Practical implicationsThe findings of the study could suggest practical implications when human resource development (HRD) professionals consider appropriate human resource interventions (e.g. training intervention) as to how to create and maintain a working environment where employees are facilitated and learned to have high levels of personal resources (i.e. self-efficacy, organizational-based self-esteem and optimism), which leads to enhancing employees’ work engagement and positive outcomes (e.g. lower turnover intention).Originality/valueGiven that little research effort has been made to investigate the relationships among personal resources (i.e. self-efficacy, organizational-based self-esteem and optimism), work engagement and turnover intention, this research contributes to the HRD literature by adding empirical evidence of the relationships in the context of Korean organizations.
A Geographic Information System‐based site selection experience for the construction of a geomagnetic observatory in Kerman Province, Iran
Authors: Izadi Yazdanabadi Marjan , Hojat Azadeh , Ranjbar Hojjatollah , Karimi Nasab Saeed 
Published: September 2017

ABSTRACTIn recent years, the necessity of constructing new geomagnetic observatories in Iran has been discussed from various aspects. Improper site selection of such important data centres can significantly affect the quality of their recorded data. In this research, site selection studies were performed to find the most favourable location to construct a geomagnetic observatory in Kerman Province, southeast of Iran. Having defined 11 site selection criteria for geomagnetic observatories, all the data layers were prepared for the whole province. After detection of seven promising regions using analytical hierarchy process and fuzzy logic method in geographical information system, Technique for Order of Preference by Similarity to Ideal Solution was used for ranking of the suitable areas. The most favourable region was finally detected southwest of Kerman Province, located between the cities of Baft and Sirjan. Detailed land surveys can be focused in this region to decide on the optimum area for the construction of the geomagnetic observatory.
Towards a geography of omnivory: Omnivores increase carnivory when sodium is limiting
Authors: Clay Natalie A. , Lehrter Richard J. , Kaspari Michael 
Published: September 2017

Abstract

Towards understanding the geography of omnivory, we tested three hypotheses that predict the proportion of animal tissue consumed: the sodium limitation hypothesis predicts that omnivores increase animal consumption in Na‐poor environments because Na bioaccumulates from plants to predators; thus, heterotrophs are Na‐rich sources. The nitrogen limitation and habitat productivity hypotheses use the same logic to predict more animal consumption in N‐poor and productive environments respectively.

Omnivory is a common trophic strategy, but what determines the balance of plant and animal tissue omnivores consume is relatively unexplored. Most of what we know comes from single populations at local scales. Here we quantitatively test these three hypotheses at a large geographic scale and across 20 species of omnivorous ants.

We tested each hypothesis using N stable isotopes (δ15N) to quantify the degree of carnivory in ant populations in 20 forests that span 12° latitude from Georgia to Maine, USA. We used the difference in δ15N between 20 ant conspecifics in 10 genera between two paired forests (10 pairs of 20 forests) that consisted of a coastal and inland forests on the same latitude to determine if the proportion of animal tissue consumed could be predicted based on Na, N or net primary productivity.

Sodium gradients accounted for 18% of the variation in δ15N, 45% if one outlier ant species was omitted. In contrast, the nitrogen limitation and habitat productivity hypotheses, which predict more animal consumption in N‐poor and more productive environments respectively, failed to vary with δ15N.

Our results reveal a geography of omnivory driven in part by access to Na.
Thermodynamically diverse syntrophic aromatic compound catabolism
Authors: Nobu Masaru Konishi , Narihiro Takashi , Liu Miaomiao , Kuroda Kyohei , Mei Ran , Liu Wen‐Tso 
Published: September 2017

SummarySpecialized organotrophic Bacteria ‘syntrophs’ and methanogenic Archaea ‘methanogens’ form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2. Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility. Although syntrophs have been generally presumed to metabolize aromatic compounds to acetate, CO2, H2 and formate, combined metagenomics and metatranscriptomics show that uncultured syntrophs utilize unconventional alternative metabolic pathways in situ producing butyrate, cyclohexanecarboxylate and benzoate as catabolic byproducts. In addition, we also find parallel utilization of diverse H2 and formate generating pathways to facilitate interactions with partner methanogens. Based on thermodynamic calculations, these pathways may enable syntrophs to combat thermodynamic restrictions. In addition, when fed with specific substrates (i.e., benzoate, terephthalate or trimellitate), each syntroph population expresses different pathways, suggesting ecological diversification among syntrophs. These findings suggest we may be drastically underestimating the biochemical capabilities, strategies and diversity of syntrophic bacteria thriving at the thermodynamic limit.
Needle and syringe programmes and opioid substitution therapy for preventing HCV transmission among people who inject drugs: findings from a Cochrane Review and meta‐analysis
Authors: Platt Lucy , Minozzi Silvia , Reed Jennifer , Vickerman Peter , Hagan Holly , French Clare , Jordan Ashly , Degenhardt Louisa , Hope Vivian , Hutchinson Sharon , Maher Lisa , Palmateer Norah , Taylor Avril , Bruneau Julie , Hickman Matthew 
Published: September 2017

AbstractAimsTo estimate the effects of needle and syringe programmes (NSP) and opioid substitution therapy (OST), alone or in combination, for preventing acquisition of hepatitis C virus (HCV) in people who inject drugs (PWID).MethodsSystematic review and meta‐analysis. Bibliographic databases were searched for studies measuring concurrent exposure to current OST (within the last 6 months) and/or NSP and HCV incidence among PWID. High NSP coverage was defined as regular NSP attendance or ≥ 100% coverage (receiving sufficient or greater number of needles and syringes per reported injecting frequency). Studies were assessed using the Cochrane risk of bias in non‐randomized studies tool. Random‐effects models were used in meta‐analysis.ResultsWe identified 28 studies (n = 6279) in North America (13), United Kingdom (five), Europe (four), Australia (five) and China (one). Studies were at moderate (two), serious (17) critical (seven) and non‐assessable risk of bias (two). Current OST is associated with 50% [risk ratio (RR) =0.50, 95% confidence interval (CI) = 0.40–0.63] reduction in HCV acquisition risk, consistent across region and with low heterogeneity (I2 = 0, P = 0.889). Weaker evidence was found for high NSP coverage (RR = 0.79, 95% CI = 0.39–1.61) with high heterogeneity (I2 = 77%, P = 0.002). After stratifying by region, high NSP coverage in Europe was associated with a 56% reduction in HCV acquisition risk (RR = 0.44, 95% CI = 0.24–0.80) with low heterogeneity (I2 = 12.3%, P = 0.337), but not in North America (RR = 1.58, I2 = 89.5%, P = < 0.001). Combined OST/NSP is associated with a 74% reduction in HCV acquisition risk (RR = 0.26, 95% CI = 0.07–0.89, I2 = 80% P = 0.007). According to Grades of Recommendation Assessment, Development and Evaluation (GRADE) criteria, the evidence on OST and combined OST/NSP is low quality, while NSP is very low.ConclusionsOpioid substitution therapy reduces risk of hepatitis C acquisition and is strengthened in combination with needle and syringe programmes (NSP). There is weaker evidence for the impact of needle syringe programmes alone, although stronger evidence that high coverage is associated with reduced risk in Europe.
Stable Control of Physiological Parameters, But Not Infection, in Preterm Lambs Maintained on Ex Vivo Uterine Environment Therapy
Authors: Miura Yuichiro , Usuda Haruo , Watanabe Shimpei , Woodward Eleanor , Saito Masatoshi , Musk Gabrielle C. , Kallapur Suhas G. , Sato Shinichi , Kitanishi Ryuta , Matsuda Tadashi , Newnham John P. , Stock Sarah J. , Kemp Matthew W. 
Published: September 2017

AbstractEx vivo uterine environment (EVE) therapy is an experimental neonatal intensive care strategy wherein gas exchange is performed by membranous oxygenators attached to the umbilical vessels. Our aim was to assess the ability of a newly refined EVE system to maintain key physiological parameters in preterm lambs within optimal ranges for 48 h. EVE group; n = 6: Preterm lambs were delivered under general anesthesia at 115 ± 2 days of gestational age. Animals were submerged in a bath of artificial amniotic fluid on EVE therapy for 48 h. Physiological parameters were monitored in real‐time over the length of the experiment. Control group; n = 11: Ewes carrying a single fetus (115 ± 2 days of gestational age) underwent recovery surgery to allow placement of a fetal carotid artery catheter. Fetuses received an infusion of sterile saline only. After euthanasia, EVE and Control group fetuses underwent necroscopy to perform static pressure–volume curves and for sampling of lung and cord blood plasma for molecular analyses. Five out of six fetuses in the EVE group completed the study period with key physiological variables remaining within their respective reference ranges for the duration of the 48 h study. Bacteremia was identified in four out of five EVE fetuses, and was associated with a systemic inflammatory response. Using our refined EVE therapy platform, preterm lambs were maintained in a stable physiological condition for 48 h. These findings represent a significant advance over earlier work with this system; however, the identification of bacteremia and a fetal inflammatory response suggests that further refinement to the EVE therapy platform is required.