bluuebunny/crossref_metadata_2025 huggingface dataset:
Looking at the map – or navigating in a virtual city interaction of visuospatial display and spatial strategies in VR
Authors: Török Zsolt Gyozo , Török Ágoston
Published: August 2018

To study geo-visualization processes a Cognitive Cartography Lab was established at Eötvös University, and the “Virtual Tourist” experiment was designed for the better understanding of actual map use during navigation. In this paper we present some preliminary results of the experiment. We explored the use of a static, north-oriented city map during navigation in an interactive, 3D town. Participants explored the virtual environment or followed verbal instructions before they completed spatial tasks. Their spatial behavior, verbal reactions were recorded, and also eye tracking data from 64 participants was collected. The experiment was designed by a multidisciplinary research group, including students of Eötvös Loránd University.
Crystal Structure of a Natural Light-Gated Anion Channelrhodopsin
Authors: Li Hai , Huang Chia-Ying , Govorunova Elena G. , Schafer Christopher T. , Sineshchekov Oleg A. , Wang Meitian , Zheng Lei , Spudich John L.
Published: August 2018

The anion channelrhodopsin GtACR1 from the alga Guillardia theta is a potent neuron-inhibiting optogenetics tool. Presented here, its X-ray structure at 2.9 Å reveals a tunnel traversing the protein from its extracellular surface to a large cytoplasmic cavity. The tunnel is lined primarily by small polar and aliphatic residues essential for anion conductance. A disulfide-immobilized extracellular cap facilitates channel closing and the ion path is blocked mid-membrane by its photoactive retinylidene chromophore and further by a cytoplasmic side constriction. The structure also reveals a novel photoactive site configuration that maintains the retinylidene Schiff base protonated when the channel is open. These findings suggest a new channelrhodopsin mechanism, in which the Schiff base not only controls gating, but also serves as a direct mediator for anion flux.
miPIE: NGS-based Prediction of miRNA Using Integrated Evidence
Authors: Peace R.J. , Hassani M. Sheikh , Green J.R.
Published: August 2018

Methods for the de novo identification of microRNA (miRNA) have been developed using a range of sequence-based features. With the increasing availability of next generation sequencing (NGS) transcriptome data, there is a need for miRNA identification that integrates both NGS transcript expression-based patterns as well as advanced genomic sequence-based methods. While miRDeep2 does examine the predicted secondary structure of putative miRNA sequences, it does not leverage many of the sequence-based features used in state-of-the-art de novo methods. Meanwhile, other NGS-based methods, such as miRanalyzer, place an emphasis on sequence-based features without leveraging advanced expression-based features reflecting miRNA biosynthesis. This represents an opportunity to combine the strengths of NGS-based analysis with recent advances in de novo sequence-based miRNA prediction. We here develop a method, microRNA Prediction using Integrated Evidence (miPIE), which integrates both expression-based and sequence-based features to achieve significantly improved miRNA prediction performance. Feature selection identifies the 20 most discriminative features, 3 of which reflect strictly expression-based information. Evaluation using precision-recall curves, for six NGS data sets representing six diverse species, demonstrates substantial improvements in prediction performance compared to miRDeep2 and miRanalyzer. The individual contributions of expression-based and sequence-based features are also examined and we demonstrate that their combination is more effective than either alone.
Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase ofStaphylococcus aureus
Authors: Monk Ian R. , Shaikh Nausad , Begg Stephanie L. , Gajdiss Mike , Lee Jean Y. H. , Pidot Sacha J. , Seemann Torsten , Kuiper Michael , Winnen Brit , Hvorup Rikki , Collins Brett M. , Bierbaum Gabriele , Howden Benjamin P. , McDevitt Christopher A. , King Glenn F. , Stinear Timothy P.
Published: August 2018

WalKR (YycFG) is the only essential two-component regulator in the human pathogenStaphylococcus aureus.WalKR regulates peptidoglycan synthesis, but this function alone appears not to explain its essentiality. To understand WalKR function we investigated a suppressor mutant that arose when WalKR activity was impaired; a single histidine to tryptophan substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PASCYT) domain of the histidine kinase WalK. Introduction of the WalKH271Ymutation into wild-typeS.aureusactivated the WalKR regulon. Structural analyses of the WalK PASCYTdomain revealed a hitherto unknown metal binding site, in which a zinc ion (Zn2+) was tetrahedrally-coordinated by four amino acid residues including H271. The WallkH271Ymutation abrogated metal binding, increasing WalK kinase activity and WalR phosphorylation. Thus, Zn2+-binding negatively regulates WalKR activity. Identification of a metal ligand sensed by the WalKR system substantially expands our understanding of this criticalS.aureusregulon.
The multi-peak adaptive landscape of crocodylomorph body size evolution
Authors: Godoy Pedro L. , Benson Roger B. J. , Bronzati Mario , Butler Richard J.
Published: August 2018

Background

Little is known about the long-term patterns of body size evolution in Crocodylomorpha, the > 200-million-year-old group that includes living crocodylians and their extinct relatives. Extant crocodylians are mostly large-bodied (3–7 m) predators. However, extinct crocodylomorphs exhibit a wider range of phenotypes, and many of the earliest taxa were much smaller (< 1.2 m). This suggests a pattern of size increase through time that could be caused by multi-lineage evolutionary trends of size increase or by selective extinction of small-bodied species. In this study, we characterise patterns of crocodylomorph body size evolution using a model fitting-approach (with cranial measurements serving as proxies). We also estimate body size disparity through time and quantitatively test hypotheses of biotic and abiotic factors as potential drivers of crocodylomorph body size evolution.

Results

Crocodylomorphs reached an early peak in body size disparity during the Late Jurassic, and underwent essentially continually decreases in disparity since then. A multi-peak Ornstein-Uhlenbeck model outperforms all other evolutionary models fitted to our data (including both uniform and non-uniform), indicating that the macroevolutionary dynamics of crocodylomorph body size are better described within the concept of an adaptive landscape, with most body size variation emerging after shifts to new macroevolutionary regimes (analogous to adaptive zones). We did not find support for a consistent evolutionary trend towards larger sizes among lineages (i.e., Cope’s rule), or strong correlations of body size with climate. Instead, the intermediate to large body sizes of some crocodylomorphs are better explained by group-specific adaptations. In particular, the evolution of a more aquatic lifestyle (especially marine) correlates with increases in average body size, though not without exceptions.

Conclusions

Shifts between macroevolutionary regimes provide a better explanation of crocodylomorph body size evolution than do climatic factors, suggesting a central role for lineage-specific adaptations rather than climatic forcing. Shifts leading to larger body sizes occurred in most aquatic and semi-aquatic groups. This, combined with extinctions of groups occupying smaller body size regimes (particularly during the Late Cretaceous and Cenozoic), gave rise to the upward-shifted body size distribution of extant crocodylomorphs compared to their smaller-bodied terrestrial ancestors.
CDK inhibitors reduce cell proliferation and reverse hypoxia-induced metastasis of neuroblastoma tumours in a chick embryo model
Authors: Swadi Rasha R. , Sampat Keerthika , Herrmann Anne , Losty Paul D. , See Violaine , Moss Diana J.
Published: August 2018

Neuroblastoma is a paediatric cancer with a poor prognosis. This is in part due to the widespread metastasis at time of presentation, which is refractory to current treatment modalities. New therapeutic agents that can control not only tumour growth but also metastasis are urgently needed.

One current therapeutic option used in the clinic is differentiation therapy with retinoic acid, where the terminal differentiation of the neuroblastoma cells reduces tumour growth in the primary tumour as well as at metastatic sites. However, retinoic acid only works in a subset of patients.

We investigated the potential of CDK inhibitors on neuroblastoma cell differentiation, tumour progression and metastasis by utilising a 3R compliant cost effective preclinical chick embryo model. In both SK-N-AS and BE(2)C cell lines, when engrafted on the chorioallantoic membrane of chick embryos, we observed a reduction of tumour cell proliferation as well as a reduction in hypoxia preconditioning-driven metastasis by 60%. In addition, the expression of a panel of genes with known roles in metastasis, which increased upon hypoxia-preconditioning, was largely reduced by a CDK1 inhibitor. These results provide a promising alternative to currently existing therapies and might aid the development of new treatment protocols for retinoic acid-resistant patients.
ADP heptose, a novel pathogen-associated molecular pattern associated with Helicobacter pylori type 4 secretion
Authors: Pfannkuch Lennart , Hurwitz Robert , Traulsen Jan , Kosma Paul , Schmid Monika , Meyer Thomas F.
Published: August 2018

The gastric pathogen Helicobacter pylori activates the NF-κB pathway in human epithelial cells via the α-kinase 1 (Alpk1)–TIFA axis. We and others have previously shown that heptose 1,7-bisphosphate (HBP) acts as a pathogen-associated molecular pattern (PAMP). HBP is an intermediate of lipopolysaccharide (LPS) synthesis in H. pylori and other gram-negative bacteria. Deletion of the hldE (rfaE) gene encoding the enzyme responsible for HBP synthesis, as well as deletion of further upstream genes, causes loss of NF-κB stimulation by H. pylori, while deletion of the downstream phosphatase encoding gene gmhB does not. This has led to the conclusion that HBP is the PAMP responsible for NF-κB induction. Here, our attempts to identify HBP in lysates of H. pylori revealed surprisingly low amounts that fail to explain NF-κB activation. Instead, we identified ADP heptose, a major downstream metabolite of HdlE, as the predominant PAMP in H. pylori lysates, exhibiting ∼100-fold stronger activity compared to HBP. It therefore appears that synthesis of ADP heptose from HBP in H. pylori occurs independently of GmhB. The data lead us to conclude that ADP heptose constitutes the key PAMP, secreted via the pathogen’s cagPAI encoded type 4 secretion (T4SS).
Is Actin Filament and Microtubule Growth Reaction- or Diffusion-Limited?
Authors: Pausch J. , Pruessner G.
Published: August 2018

Inside cells of living organisms, actin filaments and microtubules self-assemble and dissemble dynamically by incorporating actin or tubulin from the cell plasma or releasing it into their tips’ surroundings. Such reaction-diffusion systems can show diffusionor reaction-limited behaviour. However, neither limit explains the experimental data: while the offset of the linear relation between growth speed and bulk tubulin density contradicts the diffusion limit, the surprisingly large variance of the growth speed rejects a pure reaction limit. In this Letter, we accommodate both limits and use a Doi-Peliti field-theory model to estimate how diffusive transport is perturbing the chemical reactions at the filament tip. Furthermore, a crossover bulk density is predicted at which the limiting process changes from chemical reactions to diffusive transport. In addition, we explain and estimate larger variances of the growth speed.
Aperture Phase Modulation with Adaptive Optics: A Novel Approach for Speckle Reduction and Structure Extraction in Optical Coherence Tomography
Authors: Zhang Pengfei , Manna Suman K. , Miller Eric B. , Jian Yifan , Meleppat Ratheesh Kumar , Sarunic Marinko V. , Pugh Edward N. , Zawadzki Robert J.
Published: August 2018

Speckle is an inevitable consequence of the use of coherent light in optical coherence tomography (OCT), and often acts as noise that obscures micro-structures of biological tissue. We here present a novel method of suppressing speckle noise intrinsically compatible with adaptive optics (AO) in OCT system: by modulating the phase inside the imaging system pupil aperture with a segmented deformable mirror, thus producing minor perturbations in the point spread function (PSF) to create un-correlated speckle pattern between B-scans, and further averaging to wash out the speckle but maintain the structures. It is a well-controlled and universal method which can efficiently determine the optimal range of phase modulation that minimizing speckle noise while maximizing image resolution and signal strength for different systems and/or samples. As an active method, its effectiveness and efficiency were demonstrated by both ex-vivo non-biological and in-vivo biological applications.
Understanding visual attention with RAGNAROC: A Reflexive Attention Gradient through Neural AttRactOr Competition
Authors: Wyble Brad , Callahan-Flintoft Chloe , Chen Hui , Marinov Toma , Sarkar Aakash , Bowman Howard
Published: August 2018

A quintessential challenge for any perceptual system is the need to focus on task-relevant information without being blindsided by unexpected, yet important information. The human visual system incorporates several solutions to this challenge, one of which is a reflexive covert attention system that is rapidly responsive to both the physical salience and the task-relevance of new information. This paper presents a model that simulates behavioral and neural correlates of reflexive attention as the product of brief neural attractor states that are formed across the visual hierarchy when attention is engaged. Such attractors emerge from an attentional gradient distributed over a population of topographically organized neurons and serve to focus processing at one or more locations in the visual field, while inhibiting the processing of lower priority information. The model moves towards a resolution of key debates about the nature of reflexive attention, such as whether it is parallel or serial, and whether suppression effects are distributed in a spatial surround, or selectively at the location of distractors. Most importantly, the model develops a framework for understanding the neural mechanisms of visual attention as a spatiotopic decision process within a hierarchy and links them to observable correlates such as accuracy, reaction time, and the N2pc and PDcomponents of the EEG. This last contribution is the most crucial for repairing the disconnect that exists between our understanding of behavioral and neural correlates of attention.
Diatoms diversify and turn over faster in freshwater than marine environments
Authors: Nakov Teofil , Beaulieu Jeremy Michael , Alverson Andrew James
Published: August 2018

Many clades that span the marine-freshwater boundary are disproportionately more diverse in the younger, shorter-lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate-associated (benthic) lineages are several-fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden-state speciation and extinction models we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton-benthos contrast was also consistent with state-dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric, and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.
Plasticity of the electrical connectome ofC. elegans
Authors: Bhattacharya Abhishek , Aghayeva Ulkar , Berghoff Emily , Hobert Oliver
Published: August 2018

The patterns of electrical synapses of an animal nervous system (“electrical connectome”), as well as the functional properties and plasticity of electrical synapses, are defined by the neuron type-specific complement of electrical synapse constituents. We systematically examine here properties of the electrical connectome of the nematodeC. elegansthrough a genome- and nervous system-wide analysis of the expression pattern of the central components of invertebrate electrical synapses, the innexins, revealing highly complex combinatorial patterns of innexin expression throughout the nervous system. We find that the complex expression patterns of 12 out of 14 neuronally expressed innexins change in a strikingly neuron type-specific manner throughout most of the nervous system, if animals encounter harsh environmental conditions and enter the dauer arrest stage. We systematically describe the plasticity of locomotory patterns of dauer stage animals and, by analyzing several individual electrical synapses, we demonstrate that dauer stage-specific electrical synapse remodeling is responsible for specific aspects of the altered locomotory patterns as well as altered chemosensory behavior of dauer stage animals. We describe an intersectional gene regulatory mechanism, involving terminal selector and FoxO transcription factors that are responsible for inducing innexin expression changes in a neuron type- and environment-specific manner. Taken together, our studies illustrate the remarkably dynamic nature of electrical synapses on a nervous system-wide level and describe regulatory strategies for how these alterations are achieved.
Yes-associated protein (YAP) is required in maintaining normal ovarian follicle development and function
Authors: Plewes Michele R. , Hou Xiaoying , Zhang Pan , Wood Jennifer , Cupp Andrea , Davis John S.
Published: August 2018

Yes-associated protein (YAP) is one of the major components of the Hippo signaling pathway, also known as the Salvador/Warts/Hippo (SWH) pathway. Although the exact extracellular signal that controls the Hippo pathway is currently unknown, increasing evidence supports a critical role of the Hippo pathway in embryonic development, regulation of organ size, and carcinogenesis. The ovary is one of few adult tissues that exhibit cyclical changes. Ovarian follicles, the basic units of ovary, are composed of a single oocyte surrounded by expanding layers of granulosa and theca cells. Granulosa cells (GCs) produce sex steroids and growth factors, which facilitate the development of the follicle and maturation of the oocyte. It has been reported that YAP is highly expressed in human GC tumors, but the role of YAP in normal ovarian follicle development is largely unknown. In current study, we examined YAP expression in bovine ovaries. We demonstrate that downstream hippo signaling effector protein, YAP and transcription co-activator, TAZ, are present and localization of both YAP and TAZ are density-dependent. Likewise, YAP and TAZ are critically involved in granulosa cell proliferation. Furthermore, reducing YAP in granulosa cells inhibits FSH-induced aromatase expression and estradiol biosynthesis. The data suggest that YAP plays an important role in the development of ovarian follicles and estradiol synthesis, which are necessary for maintaining normal ovarian function.
Stepping up to Teaching in Business: Understanding Teaching Effectiveness for Small Classes
Authors: Paladino Angela
Published: August 2018

This article provides those teaching in small classes in an Australian tertiary environment with some recommendations on how to get started and tips for effective teaching. The focus of the advice is on small class teaching, which is generally comprised of fewer than 30 students. The tips presented are centred on being organised, understanding your content and your students, generating engagement and norms for participation, as well as investing in adaptable skill development. A seven step process to teaching effectiveness is reviewed. These tips provide teachers with foundational knowledge that can be transferred to teaching large classes.
The Longitudinal Surveys of Australian Youth: 20 Years and Beyond
Authors: Parvazian Somayeh , Semo Ronnie
Published: August 2018

The Longitudinal Surveys of Australian Youth (LSAY) follow several cohorts of young Australians as they move through secondary school, into further study, work and other destinations. The LSAY datasets provide an evidence‐based capacity for sophisticated exploration of policy and research questions through insights into individual changes, transitions and trajectories across the life‐course of young Australians. This article aims to provide an update on the progress of LSAY, including its history, evolution of the sample, sample maintenance activities, updates to the information collected, developments to the survey, the many uses that have been made of the data and possible enhancements.
The Economic Consequences of Mr Trump
Authors: Corden Max , Garnaut Ross
Published: August 2018

The Trump administration has embarked upon two large economic policy initiatives at a time of full employment: increasing the budget deficit by cutting personal and corporate tax rates; and increasing protection, especially against countries with which the United States has bilateral trade deficits. These initiatives are meant to reduce trade deficits and increase employment and incomes in the US manufacturing sector. Economic analysis tells us that the result will be larger trade deficits, and weaker total tradeables, including manufacturing employment. There may or may not be a net gain for employment and incomes in those industries which have been the greatest beneficiaries of protection. Trump's protection policies will damage incomes in the United States and the rest of the world; the damage will be greater if other countries retaliate or emulate. Alternative policies that compensate losers from free trade would give better results.
Minimum Alcohol Pricing: Balancing the ‘Essentially Incomparable’ in Scotch Whisky
Authors: Dunne Niamh
Published: August 2018

This note contrasts the approaches taken by the Court of Justice of the European Union and the UK Supreme Court in the high‐profile litigation which preceded the introduction of minimum alcohol pricing in Scotland. The case of Scotch Whisky Association and others v The Lord Advocate and another hinged, ultimately, on the necessity of minimum pricing to achieve important public health goals. The notably differing viewpoints adopted by the domestic and Union courts, however, both illustrate the elusiveness of the proportionality criterion, and expose tensions between domestic and supranational control in the context of internal market regulation.
Insane Arsonists: An Early 21st Century Sample
Authors: Leong Gregory B. , Mueller Crystal , Feldsher Mendel
Published: August 2018

We studied all individuals (n = 41) who had been found not guilty by reason of insanity for arson and who were committed to a California state psychiatric hospital on October 1, 2016 in a cross‐sectional analysis. This group of insane arsonists contained 33 (80.5%) males and eight (19.5%) females with a mean age at the time of the index arson of 35.9 years. At least 87.8% (n = 36) were considered to not have been participating in psychiatric treatment at the time of the index arson. Five (12.2%) of the insane arsonists had previously been found not guilty by reason of insanity for arson or had been convicted of having committed arson. Our findings suggest that lack of participation in psychiatric treatment was the most important factor in contributing to the index arson and the most important problem to be addressed in subsequent psychiatric treatment plans.
Impact of PD‐L1, transforming growth factor‐β expression and tumor‐infiltrating CD8+ T cells on clinical outcome of patients with advanced thymic epithelial tumors
Authors: Duan Jianchun , Liu Xidong , Chen Han , Sun Yu , Liu Yiqiang , Bai Hua , Wang Jie
Published: August 2018

Background

Advanced thymic epithelial tumors (TETs) are indolent and poorly responsive to chemotherapy. PD‐1/PD‐L1 inhibitors have shown remarkable clinical benefit in several cancers; however, many immunomodulatory molecules have been identified that affect the immune response. This study examined the progonostic roles of PD‐L1, transforming growth factor‐β (TGF‐β), and CD8+ tumor‐infiltrating lymphocytes (CD8+ TILs) in patients with TETs.

Methods

Retrospective analysis was performed on the data of 20 patients with stage IV thymic carcinoma and 13 with stage III/IV invasive thymoma. Tissue biopsies were obtained before first‐line chemotherapy was administered. Protein levels were assessed by immunohistochemistry. Objective response rate, overall survival (OS), and progression‐free survival (PFS) were analyzed.

Results

Patients with advanced thymic carcinoma exhibited higher levels of PD‐L1 and TGF‐β than patients with advanced invasive thymic carcinoma (PD‐L1: 65.0% vs. 46.2%, P = 0.472; TGF‐β: 65.0% vs. 15.4%, P = 0.011). Five advanced thymic carcinoma patients with low levels of PD‐L1 and TGF‐β exhibited high levels of CD8 staining. The median OS was 29.5 months patients with high TGF‐β expression versus 62.9 in patients with low TGF‐β (P = 0.052). In patients with advanced thymic carcinoma, the median PFS in the high PD‐L1 expression group was 13.3 months versus 23.5 (P = 0.043) in the low PD‐L1, and the median OS was 50.7 months in the high CD8 expression versus 15.1 in the CD8 low group (P = 0.154).

Conclusions

Our results showed the prognostic roles of PD‐L1, TGF‐β, and CD8+ TILs in patients with advanced TETs, and the potential for development of anti‐PD‐1/PD‐L1 therapies.
New method of lung cancer detection by saliva test using surface‐enhanced Raman spectroscopy
Authors: Qian Kun , Wang Yan , Hua Lin , Chen Anyu , Zhang Yi
Published: August 2018

Surface‐enhanced Raman spectroscopy (SERS) is a surface‐sensitive technique that enhances Raman scattering by molecules adsorbed on nanostructures. The advantages of using SERS include high detection sensibility and fast analysis, thus it is a potentially promising tool for sensing metabolic cancer molecules in trace amounts. To explore this new method of lung cancer detection, we analyzed saliva samples from 61 lung cancer patients and 66 healthy controls. An SERS system and a nano‐modified chip were used in this study. Statistics were analyzed using support vector machine (SVM) and random forest algorithms. The leave‐one‐out algorithm was used based on SVM results to analyze differences in saliva between lung cancer patients and controls. There was a significant difference between the saliva of patients with lung cancer and healthy controls using the Raman spectrum; the intensity of the spectral line in lung cancer patients was weaker than in controls and 12 characteristic peaks were detected. Saliva SERS peaks have been characterized to refer to tissues, body fluids, and biological standard Raman peaks, but it is difficult to identify molecules with current information. The sensitivity and specificity of Raman spectroscopy data and SVM classification results of lung cancer patients and normal saliva samples were both 100%. Using the leave‐one‐out algorithm, the sensitivity was 95.08% and the specificity was 100%. The sensitivity of the random forest method was 96.72% and specificity was 100%. Our results show that SERS has the potential to detect lung cancer.
Assessing adequacy of models of phyletic evolution in the fossil record
Authors: Voje Kjetil Lysne
Published: August 2018

Comparing relative fit of different models of evolutionary dynamics to time series of phyletic change is a common tool when interpreting the fossil record. However, a measure of relative fit is no guarantee the preferred model describes the data well. Selecting a good model is essential for robust inferences, but we are currently lacking tools to investigate if a model of phyletic evolution represents an adequate description of trait dynamics in fossil data.

This study develops a general statistical framework implemented in R for assessing the adequacy of the three most commonly used models of evolution in the fossil record; stasis, directional change and random walk. The statistical framework is applied to 300 fossil time series in order to assess how often the three models represent adequate descriptions of evolutionary dynamics in the fossil record.

The model that showed the best relative fit to a particular fossil time series (using AICc) passed all adequacy tests in 219 out of 300 cases (73%, directional trend = 76%, stasis = 64%, random walk = 81%). It is therefore not uncommon that the best model according to AICc does not adequately describe the trait dynamics in a fossil time series.

Statistical tests of model adequacy ease evaluation of whether a particular model is a good descriptor of phyletic evolution and can assist in making meaningful inferences of model parameters (e.g., as rates of evolution) and interpretations of evolution in the fossil record.
Not all data are equal: Influence of data type and amount in spatial conservation prioritisation
Authors: Kujala Heini , Lahoz‐Monfort José Joaquín , Elith Jane , Moilanen Atte
Published: August 2018

Decisions about land use significantly influence biodiversity globally. The field of spatial conservation prioritisation explores allocation of conservation effort, including for reserve network expansion, targeting habitat restoration, or minimising ecological impacts of development. Inevitably, the utility of such planning depends on the quantity and quality input data, including spatial information on biodiversity, threats, and cost of action. In this work we systematically develop understanding about the significance of these different data types in spatial conservation prioritisation.

We clarify the common ways different data types enter an analysis, develop mathematical models to understand the effects of data in spatial prioritisation, and survey literature to establish typical quantities of different types of data used. We use Jackknife analysis to derive the expected change in site values, when a single new data layer is added to a prioritisation. We validate mathematical formulae for expected impacts using simulations.

A survey of scientific literature reveals that typical spatial prioritisation analyses include hundreds of biodiversity feature layers (species, habitat types, ecosystem services), but the count of cost, threat or habitat condition layers is typically 0–5. Due to these differences, and the mathematical formulations commonly used to combine data types, the influence of a single cost, threat, or habitat condition data layer can be an order or two higher than the influence of a single biodiversity feature layer. In a classical cost‐effectiveness formulation (benefits divided by costs, B/C) the influence of a single cost layer can even be as large as the joint influence of thousands of species distributions. We also clarify how changes in data impact site values and spatial priority rankings differently, with the latter being further influenced by data correlations, the spread of numeric values inside data layers and other data characteristics. For example, costs influence priorities significantly if cost is positively correlated with biodiversity, but the correlation is the other way around for biodiversity and habitat condition.

This work helps conservation practitioners to direct efforts when collating data for spatial conservation planning. It also helps decision makers understand where to focus attention when interpreting conservation plans and their uncertainties.
Inflammaging impairs peripheral nerve maintenance and regeneration
Authors: Büttner Robert , Schulz Alexander , Reuter Michael , Akula Asha K. , Mindos Thomas , Carlstedt Annemarie , Riecken Lars B. , Baader Stephan L. , Bauer Reinhard , Morrison Helen
Published: August 2018

The regenerative capacity of peripheral nerves declines during aging, contributing to the development of neuropathies, limiting organism function. Changes in Schwann cells prompt failures in instructing maintenance and regeneration of aging nerves; molecular mechanisms of which have yet to be delineated. Here, we identified an altered inflammatory environment leading to a defective Schwann cell response, as an underlying mechanism of impaired nerve regeneration during aging. Chronic inflammation was detected in intact uninjured old nerves, characterized by increased macrophage infiltration and raised levels of monocyte chemoattractant protein 1 (MCP1) and CC chemokine ligand 11 (CCL11). Schwann cells in the old nerves appeared partially dedifferentiated, accompanied by an activated repair program independent of injury. Upon sciatic nerve injury, an initial delayed immune response was followed by a persistent hyperinflammatory state accompanied by a diminished repair process. As a contributing factor to nerve aging, we showed that CCL11 interfered with Schwann cell differentiation in vitro and in vivo. Our results indicate that increased infiltration of macrophages and inflammatory signals diminish regenerative capacity of aging nerves by altering Schwann cell behavior. The study identifies CCL11 as a promising target for anti‐inflammatory therapies aiming to improve nerve regeneration in old age.
Dissecting folliculitis (dissecting cellulitis) of the scalp: a 66‐patient case series and proposal of classification
Authors: Lee Chaw‐Ning , Chen WenChieh , Hsu Chao‐Kai , Weng Tzu‐Teng , Lee Julia Yu‐Yun , Yang Chao‐Chun
Published: August 2018

Background and Objectives

Dissecting folliculitis (DF) or dissecting cellulitis of the scalp is regarded as a rare disease with disfiguring scarring alopecia. This study aimed to analyze the features of DF and to propose a classification to define its severity.

Patients and Methods

A hospital‐based retrospective study was conducted. Patients with a histopathological diagnosis or clinical features leading to diagnosis of DF were included and classified into three stages.

Results

Among the 66 patients recruited (63 men / 3 women, mean age 24.9 years), multiple interconnected alopecic nodules involving the vertex scalp were the main feature. Histopathology showed an extensive inflamed granulation abscess forming a dissection plane in the lower dermis/subcutis in the acute stage. Lymphocytic infiltration was predominant in seven of 21 histology specimens. Overweight and obesity were noted in 29 of 45 patients examined. No association with smoking was found. There was comorbidity with acne conglobata in 15 of 66 patients, two of whom had acne inversa. Longer disease duration and greater number of nodules were associated with higher severity of DF (p < 0.05). A complete remission rate of 25 % was achieved by any treatment, and a rate of 37.5 % was achieved with oral isotretinoin alone.

Conclusions

DF is not uncommon in Taiwan. An association with obesity needs to be clarified.
Wheat as a dual crop for biorefining: Straw quality parameters and their interactions with nitrogen supply in modern elite cultivars
Authors: Jørgensen Henning , van Hecke Jan , Zhang Heng , Malik Pernille L. , Felby Claus , Schjoerring Jan K.
Published: August 2018

Agricultural residues, such as straw, offer an opportunity to produce biofuels and chemicals in biorefineries without compromising food production. The ideal “dual‐purpose cultivar” would have high yield of grain and straw. In addition, the straw should be easy to process in a biorefinery: It should have good degradability, high concentration of carbohydrates, and low concentration of ash. Nitrogen (N) is an essential nutrient important for plant growth, crop yield and grain quality. However, N production and application comes with a high cost and high environmental footprint. The N application should consequently be based on an economical optimum. Limited knowledge exists on how N application affects the potential of straw for biorefining, for example, straw yield and quality. This study, conducted over three cropping seasons, investigated the effect of N supply on the biorefining potential and included 14 wheat cultivars and one triticale cultivar. The N supply directly affected the yield of straw and grain. In addition, the protein concentration in grain and straw increased, but the composition of the straw with respect to carbohydrates and lignin was largely unaffected by N supply. The only significant change was a lower silicon concentration at increasing N application rate, which could be beneficial for lignin valorization in biorefineries. Likely due to the negligible changes in cell wall composition, the effect of N application rate on straw degradability was not significant. N application should therefore primarily be optimized with respect to grain quality and overall yield of grain and straw. Differences between cultivars were also minor with respect to their performance in a biorefinery process. From a breeding and agronomic perspective, focus should therefore be put on maximizing the biomass output from the field, that is, selecting the cultivar with highest grain and straw yield and optimizing the application of fertilizer to get optimum N use efficiency.
Is plaque regrowth inhibited by dentifrice?
Authors: Valkenburg Cees , Van der Weijden Fridus , Slot Dagmar Else
Published: August 2018

Objectives

The aim of this systematic review was to establish in studies with human participants the effect of a regular fluoride dentifrice compared to water or saline on dental plaque inhibition.

Methods

MEDLINE‐PubMed, Cochrane‐CENTRAL, EMBASE and other electronic databases were searched, up to April 2018. The inclusion criteria were controlled clinical trials among participants aged ≥18 years with good general health. Papers that evaluated the effect of dentifrice slurry compared with water or saline on plaque regrowth during a 4‐day nonbrushing period were included. Data were extracted from the eligible studies, the risk of bias was assessed, and a meta‐analysis was performed where feasible.

Result

The search retrieved eight eligible publications including 25 comparisons. The estimated potential risk of bias was low for all studies. Based on three different indices, overall plaque regrowth was significantly (P < 0.01) inhibited for 0.25 or more by the use of a dentifrice slurry as compared to water. All subanalysis on specific dentifrice ingredients and the overall descriptive analysis supported these findings.

Conclusion

The results of this review demonstrate moderate‐quality evidence for a weak inhibitory effect on plaque regrowth in favour of the use of a dentifrice intended for daily use.
ON THE TIMING OF PRODUCTION DECISIONS IN MONETARY ECONOMIES
Authors: Anbarci Nejat , Dutu Richard , Sun Ching‐Jen
Published: August 2018

In most macroeconomic models inflation tends to be harmful. In this article, we show that by simply changing the timing of production decisions by firms from “on demand” to “in advance,” some inflation can boost welfare as long as goods are sufficiently perishable. The main conclusion from this research is that by effectively hiding the strategic interaction between supply and demand, assuming production on demand is not without loss of generality.
Specific foot health‐related quality‐of‐life impairment in patients with type II versus type I diabetes
Authors: Palomo‐López Patricia , Losa‐Iglesias Marta Elena , Becerro‐de‐Bengoa‐Vallejo Ricardo , López‐López Daniel , Rodríguez‐Sanz David , Romero‐Morales Carlos , Calvo‐Lobo César
Published: August 2018

The aims of this research were to evaluate and compare the effect in a matched sample of patients with type II and type I diabetes scores using a specific quality‐of‐life (QoL) tool related to overall and foot health (Foot Health Status Questionnaire [FHSQ]). A sample of 62 patients with an age median of 59.00 ± 19.00 y were divided into type I (n = 31) and type II (n = 31) diabetes groups. Socio‐demographics data include: (1) age, (2) gender, (3) body mass index, (4) professional activity, (5) study level, and (6) civil status. The FHSQ was used to evaluate foot (pain, function, footwear, and general health section I domains) and overall (general health, social capacity, physical activity, and vigour section II domains) health related to QoL. Differences between groups were assessed by means of a t test or Mann‐Whitney U test for independent samples. There were no statistically significant differences (P > 0.05) for any socio‐demographic data. Regarding the FHSQ section II of the specific foot health‐related QoL, the only statistically significant differences (P = 0.042) were observed for the general foot health showing a QoL impairment (lower median ± interquartile range) in patients diagnosed with type II diabetes (60.00 ± 60.00 points) compared with patients who suffered from type I diabetes (25.00 ± 72.50 points). The other domains did not show any statistically significant differences (P > 0.05). Patients with type II diabetes present a negative impact on the specific foot health‐related QoL compared with patients who suffered from type I diabetes.
Rethinking EU Governance: From ‘Old’ to ‘New’ Approaches to Who Steers Integration*
Authors: Schmidt Vivien A.
Published: August 2018

EU scholars have long been divided on the main drivers of European integration. The original approaches were at odds on whether EU level intergovernmental actors or supranational actors were better able to exercise coercive or institutional power to pursue their interests, with Andrew Moravcsik's liberal intergovernmentalism serving as a baseline for one side of those debates. Newer approaches are similarly divided, but see power in terms of ideational innovation and consensus‐focused deliberation. The one thing old and new approaches have in common is that they ignore the parliamentarists, new and old. What all sides to the debates have failed to recognize is the reality of a ‘new’ EU governance of more politically charged dynamics among all three main EU actors exercising different kinds of power. This has roots not only in the national level's increasing ‘politics against policy’ and its bottom up effects on the EU level. It also stems from EU institutional interactions at the top, and its ‘policy with politics’.
Chronic radial artery occlusion does not cause exercise induced hand ischemia
Authors: van der Heijden Dirk J. , van Leeuwen Maarten A.H. , Ritt Marco J.P.F. , van de Ven Peter M. , van Royen Niels
Published: August 2018

Objectives

The aim of the study was to evaluate the occurrence of hand ischemia in patients with radial artery occlusion (RAO), using the contralateral hand as control.

Background

Radial artery occlusion is a common complication (6%) after transradial access (TRA) but rarely leads to major ischemic events due to the collateral perfusion of the hand. However, it has been reported that RAO can become symptomatic, possibly as a consequence of hand ischemia. To evaluate the existence of exercise induced hand ischemia in patients with RAO, we initiated the present study.

Methods

After a transradial coronary procedure, patients with suspicion of RAO were asked for study participation. After informed consent, radial ultrasound was performed. In patients with confirmed RAO, rest perfusion of the digits was analyzed by laser Doppler digital imaging. Occurrence of ischemia during exercise was assessed with transcutaneous oxygen pressure (TcPO2) and thumb capillary lactate. All analyses were performed in both the RAO side as well as the contralateral side as control.

Results

RAO occlusion was confirmed in 18 patients. After 5 min of exercise there were no significant differences in TcPO2 (51.4 mmHg [±17.2] vs 43.9 mmHg [±15.5], P = 0.18) or lactate (2.0 mmol/L [±0.7] vs 2.1 mmol/L [±0.7], P = 0.80) between RAO side and control side. Differences in mean TcPO2 were found to be stable during exercise and not different from baseline differences.

Conclusions

Chronic radial artery occlusion does not lead to exercise induced hand ischemia.
A Review of locomotor diversity in mammals with analyses exploring the influence of substrate use, body mass and intermembral index in primates
Authors: Granatosky Michael C.
Published: August 2018

Locomotor diversity has meant many different things depending on the subject area or investigator. While no concrete definition of locomotor diversity is currently available, this has not stopped researchers from making a number of assertions about the underlying mechanisms that determine whether a species will have high or low locomotor diversity. Some of these claims include that: (1) arboreal primates demonstrate higher locomotor diversity than terrestrial species; (2) anatomically generalized and small‐bodied primates demonstrate higher locomotor diversity than anatomically specialized and large‐bodied taxa; and (3) primates demonstrate higher locomotor diversity compared to non‐primate mammals. None of these claims have been tested in any sort of comparative framework. Using previously published locomotor repertoire data from 110 mammalian species, this study co‐opted the Shannon–Wiener diversity index to calculate a singular measure of locomotor diversity. Phylogenetic analyses of these locomotor diversity indices reveal that within primates, small‐bodied species demonstrate greater locomotor diversity than large‐bodied taxa. However, this effect becomes non‐significant when accounting for differences in substrate‐use (i.e. arboreal vs. terrestrial). Anatomical specialization has no effect on locomotor diversity in primates. Furthermore, primates do not inherently have greater locomotor diversity than other mammalian taxa. Findings from this study suggest that movement on arboreal substrates requires all mammals, regardless of taxonomic affiliation, to demonstrate high locomotor diversity. These data further highlight the challenges faced by arboreal animals and raise the possibility that being able to switch fluidly and frequently between many different locomotor modes may be advantageous for animals moving in an arboreal milieu.
Pronominal anaphora, coreference, and closed quotation marks
Authors: Gasparri Luca
Published: August 2018

Consider the following sentence: “Mary meditated on the sentence ‘Bill is a good friend’ and concluded that he was a good friend.” It is standardly assumed that in sentences of this sort, containing so‐called “closed” quotations, the expressions occurring between quotation marks are mentioned and do not take their ordinary referents. The quoted NP “Bill” refers, if anything, to the name ‘Bill,’ not to the individual Bill. At the same time, the pronoun “he,” apparently anaphoric on quoted “Bill,” refers to the individual Bill. The case seems thus to invalidate the intuitive principle that pronouns anaphoric on referential expressions inherit their reference from their antecedents. The paper formulates the argument, argues that sentences exhibiting the described pattern do not constitute evidence against the intuitive principle, and proposes an alternative account of the anaphoric relation involved.