bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase-coherence classification: a new wavelet-based method to separate local field potentials into local (in)coherent and volume-conducted components
Authors: von Papen M. , Dafsari H. , Florin E. , Gerick F. , Timmermann L. , Saur J. 
Published: November 2016

AbstractLocal field potentials (LFP) reflect the integrated electrophysiological activity of a large group of neurons. To minimize influence of external activity on the analysis, conventionally bipolar recordings are used to eliminate volume-conducted signals. Here we introduce a novel method, called phase-coherence classification (PCC), to separate LFP in time-frequency domain into a volume-conducted, a local incoherent and local coherent signal. The PCC allows to compute the power spectral densities of each signal and to associate each class with possible locations of electro-physiological activity. In order to test the resolution properties and accuracy of the method we generate composite and non-stationary synthetic time series with similar statistical characteristics as measured LFP. The PCC identifies volume-conducted signals with a phase threshold that is determined from probability density functions of non-phase-shifted synthetic time series. We estimate optimal PCC parameters for the analysis of beta band oscillations in LFP and apply the PCC to a test data set obtained from within the subthalamic nucleus of eight patients with Parkinson’s disease (PD). We show that PCC can identify activity of multiple local clusters during a tremor episode and quantify the relative power of local and volume-conducted signals. We further analyze the electrophysiological response to an apomorphine injection during rest and show that incoherent activity in the low beta band shows a significant medication-induced decrease. We further find significant movement-induced changes on medication of the local coherent signal, which increased during an isometric hold task and decreased during phasic wrist movement. This indicates a different role of incoherent and coherent signals possibly related to physiologically different networks. This new PCC method can potentially also be applied to EEG and MEG data in order to minimize the influence of spatial leakage on power spectra and coherence estimates.
FastSKAT: Sequence kernel association tests for very large sets of markers
Authors: Lumley Thomas , Brody Jennifer , Peloso Gina , Morrison Alanna , Rice Kenneth 
Published: November 2016

AbstractThe Sequence Kernel Association Test (SKAT) is widely used to test for associations between a phenotype and a set of genetic variants, that are usually rare. Evaluating tail probabilities or quantiles of the null distribution for SKAT requires computing the eigenvalues of a matrix related to the genotype covariance between markers. Extracting the full set of eigenvalues of this matrix (ann×nmatrix, fornsubjects) has computational complexity proportional ton3. As SKAT is often used whenn> 104, this step becomes a major bottleneck in its use in practice. We therefore propose fastSKAT, a new computationally-inexpensive but accurate approximations to the tail probabilities, in which theklargest eigenvalues of a weighted genotype covariance matrix or the largest singular values of a weighted genotype matrix are extracted, and a single term based on the Satterthwaite approximation is used for the remaining eigenval-ues. While the method is not particularly sensitive to the choice of k, we also describe how to choose its value, and show how fastSKAT can automatically alert users to the rare cases where the choice may affect results. As well as providing faster implementation of SKAT, the new method also enables entirely new applications of SKAT, that were not possible before; we give examples grouping variants by topologically assisted domains, and comparing chromosome-wide association by class of histone marker.
Pharmaceutical efficacy of human epiphyseal chondrocytes with differential replication numbers for cellular therapy products
Authors: Nasu Michiyo , Takayama Shinichiro , Umezawa Akihiro 
Published: November 2016

AbstractThe cell-based therapy for cartilage or bone requires a large number of cells serial passages of chondrocytes are, therefore, needed. However, fates of expanded chondrocytes from extra fingers remains unclarified. The chondrocytes from human epiphyses morphologically changed from small polygonal cells, to bipolar elongated spindle cells and to large polygonal cells with degeneration at early passages. Gene of type II collagen was expressed in the cells only at a primary culture (Passage 0) and Passage 1 (P1) cells. The nodules by implantation of P0 to P8 cells were composed of cartilage and perichondrium. The cartilage consisted of chondrocytes with round nuclei and type II collagen-positive matrix, and the perichondrium consisted of spindle cells with type I collage-positive matrix. The cartilage and perichondrium developed to bone with marrow cavity through enchondral ossification. Chondrogenesis and osteogenesis by epiphyseal chondrocytes depended on replication number in culture. It is noteworthy to take population doubling level in correlation with pharmaceutical efficacy into consideration when we use chondrocytes for cell-based therapies.
Gentle, fast and effective crystal soaking by acoustic dispensing
Authors: Collins Patrick M , Tsing Ng Jia , Talon Romain , Nekrosiute Karolina , Krojer Tobias , Douangamath Alice , Brandao-Neto Jose , Wright Nathan , Pearce Nicholas M , von Delft Frank 
Published: November 2016

SynopsisA high-throughput method is described for crystal soaking using acoustic droplet ejection, and its effectiveness demonstrated.AbstractBright light sources, agile robotics, and fast detectors are continually reducing the time it takes to perform an X-ray diffraction experiment, making high throughput experiments more feasible than ever. But this is also pushing the upstream bottleneck towards sample preparation, even for robust and well characterised crystal systems. Crystal soaking is routinely used to generate protein-ligand complex structures, yet protein crystals are often sensitive to changes in solvent composition, and frequently require gentle or careful stepwise soaking techniques, limiting overall throughput. Here, we describe the use of acoustic droplet ejection for soaking of protein crystals with small molecules, and show that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 minutes. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables targeted placement of the compound/solvent away from crystals and towards drop edges, allowing for gradual diffusion of solvent across the drop. This ensures both an improvement in reproducibility of X-ray diffraction and an increased solvent tolerance of the crystals, thus enabling higher effective compound soaking concentrations. We detail the technique here with examples from the protein target JMJD2D, a histone lysine demethylase, having roles in cancer and the focus of active structure based drug design efforts.
Phylogenetic analysis suggests joint control of transmission mode in a grass-endophyte symbiosis
Authors: Brown Alexandra , Akçay Erol 
Published: November 2016

AbstractHow symbionts are transmitted between hosts is key to determining whether symbioses evolve to be harmful or beneficial. Vertical transmission favors mutualistic symbionts, and horizontal transmission more virulent ones. Transmission mode evolution itself depends on whether the host or symbiont can respond to selection on transmission mode. When hosts control the transmission mode, vertical transmission should evolve under more restrictive circumstances than when symbionts are in control. We take a phylogenetic approach to determine whether the host, symbiont, or both control transmission mode using the pooid grass-epichloid endophyte symbiosis as a model system. This study is the first to investigate control of transmission mode evolution in a phylogenetic context. We find a signal of host phylogeny but only in conjunction with symbiont identity. This pattern suggests joint control of transmission mode by the host and symbiont. It also suggests that non-genetic or non-conserved symbiont traits may determine whether host traits lead to vertical or horizontal transmission.
Histone code and higher-order chromatin folding: A hypothesis
Authors: Prakash Kirti , Fournier David 
Published: November 2016

AbstractHistone modifications alone or in combination are thought to modulate chromatin structure and function; a concept termed histone code. By combining evidence from several studies, we investigated if the histone code can play a role in higher-order folding of chromatin. Firstly using genomic data, we analyzed associations between histone modifications at the nucleosome level. We could dissect the composition of individual nucleosomes into five predicted clusters of histone modifications. Secondly, by assembling the raw reads of histone modifications at various length scales, we noticed that the histone mark relationships that exist at nucleosome level tend to be maintained at the higher orders of chromatin folding. Recently, a high-resolution imaging study showed that histone marks belonging to three of the five predicted clusters show structurally distinct and anti-correlated chromatin domains at the level of chromosomes. This made us think that the histone code can have a significant impact in the overall compaction of DNA: at the level of nucleosomes, at the level of genes, and finally at the level of chromosomes. As a result, in this article, we put forward a theory where the histone code drives not only the functionality but also the higher-order folding and compaction of chromatin.
CFOs’ views on corporate financing decisions
Authors: Yatiwelle Koralalage Weerakoon Banda 
Published: November 2016

Purpose
The purpose of this paper is to examine the managerial views on the corporate financing practices of firms in the emerging market of Sri Lanka.

Design/methodology/approach
A survey approach was employed using chief financial officers (CFOs) from the top non-financial firms listed on the Colombo Stock Exchange.

Findings
CFOs’ views on corporate financing practices are not fully consistent with the theory: financial hierarchy appears to be more important and firms are less leveraged. Most Sri Lankan CFOs perceive some policy factors as important and theoretically support: volatility of earnings and cash flows, tax advantages of interest deductibility, transaction costs, timing of interest rates, low foreign interest rates and debt equity targets. These factors are high priority in emerging markets but either not important at all or less important in developed markets. Matching debt maturity with the life of assets is equally important in both markets. Most CFOs adhere their financing to the local debt market, while a few firms use foreign debt. CFOs are concerned about earnings per share (EPS) dilution, providing a natural hedge in foreign debt issues, credit ratings, under/overvaluation of stocks and corporate control, whereas they are significantly important in developed markets. Age and education mostly explain the differences.

Research limitations/implications
The study is restricted to large companies in a relatively smaller market. Hence, sample size is relatively small, even though it shows a higher response rate.

Practical implications
The study offers insights for corporate financing decision-makers that could impact on firm value through a shift in emphasis toward capital structure theories.

Originality/value
The paper focuses on corporate financing practices in Sri Lanka in search of emerging market features that could mitigate the gap in the emerging market literature through survey evidence.
How can the tourism industry respond to the global challenges arising from climate change and environmental degradation?
Authors: Nair Vikneswaran , Mohamed Badaruddin , Thomas Toney K. 
Published: November 2016

Purpose
The aim of this paper is to critically review the contribution made by this theme issue in responding to the strategic question: “How can the tourism industry respond to the global challenges arising from climate change and environmental degradation?”

Design/methodology/approach
A critical content analysis of the papers selected for the theme issue was undertaken to learn from the best practices globally. This enabled the theme editors to reflect on the rationale for the theme issue question, the starting-point and the editorial process.

Findings
This summary paper highlights the most significant outcomes from the theme issue in terms of the contributions to knowledge and/or professional practice. It also summarizes the implications for management action and applied research arising from the outcomes and best practices based on case studies in Malaysia, Canada and New Zealand. As the main objective of the theme issue was to obtain a general overview of the relationship between tourism and climate change, five general review papers were included to strengthen the research framework.

Research limitations/implications
This paper outlines the challenges and new approaches in dealing with the issue of climate change. Given the economic, social and environmental significance of tourism, coverage of the climate change issue as it relates to tourism is, yet, limited. Given this scenario, the theme issue has contributed to the body of knowledge in this important field.

Originality/value
This paper explores the extent to which the cases presented and the review of various climate change concepts can provide guidance. The approaches and issues discussed in this theme issue could be replicated and applied in countries that are beginning to focus on climate change issues.
Community participation in mitigating marine waste to reduce climatic change in tourism destinations
Authors: Prabhakaran Sudesh , Nair Vikneswaran , Ramachandran Sridar 
Published: November 2016

Purpose
Waste in the marine environment has become a serious task to be managed. Uncontrolled dumping creates large amounts of methane gas contributing to greenhouse gas emissions. This conceptual paper focuses on the role of community in waste management activities to reduce carbon emissions in the marine environment. Hence, this paper aims to examine using literature, the various roles of community, types of marine waste and its impact on carbon emissions and climate change.

Design/methodology/approach
The paper is based on evaluation and criticism from previous studies and provides a hypothetical understanding of the human contribution to climate change, and its impacts which will increasingly affect climate change and sustainable tourism.

Findings
The results from this study can be used as a guide for policy makers to help improve community participation and public engagement in efforts to reduce the levels of waste in the marine environment. This is especially critical in rural tourism destinations where the impact of uncontrolled marine waste has serious consequences for the tourism industry.

Originality/value
The paper contributes to a better understanding of the role of community in mitigating waste to attain a higher quality of tourism experience and environmental benefits from emission level reductions.
Anti‐epiphyte defences in the red seaweed Gracilaria vermiculophylla: non‐native algae are better defended than their native conspecifics
Authors: Wang Shasha , Wang Gaoge , Weinberger Florian , Bian Dapeng , Nakaoka Masahiro , Lenz Mark 
Published: November 2016

Summary

Epibiosis in the marine environment is a stressor that may determine invasion success in introduced species. Previous comparisons showed resistance to epibionts can be higher in non‐native than in resident seaweed species, but we do not know whether it is an intrinsic trait of the non‐natives or it has been acquired during the invasion process. To elucidate this question, a comparison between native and non‐native populations of the same species is needed.

Resistance against two groups of epiphytes was assessed in living thalli and in artificial substrata coated with surface extracts, both gained from four Asian (native) and four European (non‐native) populations of the red alga Gracilaria vermiculophylla. Two diatom species and two filamentous macroalgae were used as micro‐ and macro‐epiphytes, and one of each type was collected in Asia, while the other came from Europe. Laboratory assays were done in both distributional ranges of G. vermiculophylla and in different seasons. We used G. vermiculophylla from four populations in each range and used a fully crossed design with the factors (i) ‘Origin of Gracilaria’, (ii) ‘Origin of epiphytes’, (iii) ‘Season’ and (iv) ‘Solvent used for extraction’.

Both groups of epiphytes, regardless of their origin, attached less to living thalli and to surface extracts from non‐native G. vermiculophylla. Fewer diatoms attached to hexane‐based extracts, while fewer Ceramium filaments settled on extracts gained with dichloromethane.

Synthesis. Our results show for the first time that non‐native individuals of a marine organism are better defended against epiphytes than native conspecifics. Furthermore, we found evidence that at least a part of the defence is based on extractable secondary metabolites. We discuss several mechanisms that could explain the increased resistance to epiphytes in non‐native individuals, including the release from enemies in the non‐native range, which could lead to an increase in algal performance during the invasion process. We suggest that an enhanced defence against epiphytes after introduction is one reason for G. vermiculophylla's invasion success. Our observation may also apply to other basibiont–epibiont and host–enemy systems, including plant–plant, plant–animal and animal–animal interactions, in aquatic environments and could be a key feature of bioinvasions.
Changes in spatial variance during a grassland to shrubland state transition
Authors: Ratajczak Zak , D'Odorico Paolo , Nippert Jesse B. , Collins Scott L. , Brunsell Nathaniel A. , Ravi Sujith 
Published: November 2016

Summary

State transitions are changes in ecosystem structure and self‐reinforcing feedbacks that are initiated when an exogenous driver variable crosses a threshold. Reversing state transitions is difficult and costly. While some state transitions are relatively rapid, many take years to decades. Outside of theoretical models, very little is known about slower state transitions and how they unfold in time and space.

We quantified changes in spatial variance as a mesic grassland ecosystem shifts to a shrub‐dominated state, using long‐term experiments and simulations that maintain grasslands with annual fires or initiate a state transition to shrub dominance by decreasing fire frequency.

In the experiments, the susceptibility to state transitions varied substantially in space. In the less frequent fire treatment, some plots became shrub‐dominated around year 20 and grass extirpations began in year 25, but a third of the plots were still grass‐dominated in year 37. Variable rates of state transition resulted in increasing spatial variance of grass cover over time, whereas shrub cover variance decreased. In the annually burned treatment, grasses remained dominant and the spatial variance of grass cover declined.

In a separate experiment, less frequent fires were maintained for 23 years and then switched to annual fires. The switch to annual fires occurred shortly after grass variance started to increase and a majority of these plots quickly returned to a grass dominated state.

In simulations, spatial variance remained low and average grass cover was high under frequent fires. If fire frequency decreased below a threshold, the ecosystem transitioned to shrubland, with a transient increase in the spatial variance of grass cover during the transition between states.

Synthesis. Spatial variability in the rate and susceptibility to state transitions is indicative of a system with a patchy spatial structure, high spatial heterogeneity and low connectivity between patches. Increases in spatial variance can serve as an indication that some patches have begun a state transition and that management interventions are needed to avoid widespread transitions. This is one of the first empirical examples where altering management after an increase in spatial variance prevented state transitions.
An assessment of carbon and nutrient limitations in the formation of the southern Andes tree line
Authors: Fajardo Alex , Piper Frida I. 
Published: November 2016

Summary

Although the principal mechanism determining tree line formation appears to be carbon (C)‐sink limitations due to low temperatures, few studies have assessed the complementary role of reduced soil nutrient availability with elevation. We tested the hypothesis that nutrient (especially nitrogen, N) limitations at tree line may directly (via C‐source) or indirectly (via C‐sink) reduce the growth of a winter deciduous tree line species.

If a shortage of soil N with elevation is involved in tree line formation, it should occur in two alternative ways: (i) through sink limitations because N is required for tissue formation, which would indirectly limit C investments (N decreases and C reserves increase with elevation), and (ii) through C limitations because this would lead directly to a reduction of photoassimilates (N and C reserves decrease with elevation).

In testing our hypothesis, we analysed tree growth rates (basal area increment), twig non‐structural carbohydrate (NSC) and N concentrations, leaf N, phosphorus (P), N:P ratio concentrations, and soil nutrient levels (NO3−, NH4+, Olsen–P) in four disparate climate and soil Nothofagus pumilio tree lines spanning 18 degrees of latitude in the southern Andes of Chile.

We found a significant decrease in tree growth with elevation. Twig NSC concentrations pooled across locations also decreased significantly with elevation (starch constituted most of the NSC and was highly responsible for the negative trend), although this trend was mostly driven by the northernmost locations. Contrary to soil N availability, leaf N and P concentrations increased significantly with elevation. Twig N concentrations, soil P and leaf N:P ratios did not change with elevation.

Synthesis. The elevational decrease in NSC concentrations supports C‐source limitation in N. pumilio trees at tree line elevation. In the light of this, we assert that the current global explanation for tree line formation (C‐sink‐limitation driven by low temperatures) must be revisited. Given that leaf N and P concentrations increased and twig N concentrations did not change with elevation, nutrient limitation is not likely to be involved in the C‐limitations and could not therefore be an explanation for tree line formation.
Formation of propionate and butyrate by the human colonic microbiota
Authors: Louis Petra , Flint Harry J. 
Published: November 2016

SummaryThe human gut microbiota ferments dietary non‐digestible carbohydrates into short‐chain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of health‐promoting functions. Here an overview of the metabolic pathways utilized by gut microbes to produce these two SCFA from dietary carbohydrates and from amino acids resulting from protein breakdown is provided. This overview emphasizes the important role played by cross‐feeding of intermediary metabolites (in particular lactate, succinate and 1,2‐propanediol) between different gut bacteria. The ecophysiology, including growth requirements and responses to environmental factors, of major propionate and butyrate producing bacteria are discussed in relation to dietary modulation of these metabolites. A detailed understanding of SCFA metabolism by the gut microbiota is necessary to underpin effective strategies to optimize SCFA supply to the host.