bluuebunny/crossref_metadata_2025_split huggingface dataset:
The differentially expressed translationally controlled tumor proteins TCTP1 and TCTP2 inTrypanosoma brucei
Authors: Jojic Borka , Amodeo Simona , Ochsenreiter Torsten 
Published: September 2017

1.SummaryInTrypanosoma bruceiwe identified two TCTP genes differentially expressed during the parasite life cycle and discovered the mechanism by which this expression is controlled. Furthermore, we demonstrate that TCTP is important for cell growth as well as proper cell and organelle morphology in the insect form of the parasite.2.AbstractTCTP is a highly conserved protein ubiquitously expressed in eukaryotes. Studies have reported TCTP to be involved in growth and development, cell cycle progression, protection against cellular stresses and apoptosis, indicating the multifunctional role of the protein. Here, for the first time we characterize the expression and function of TCTP in the unicellular parasiteTrypanosoma brucei. We identified two paralogue TCTP genes, which we named TbTCTP1 and TbTCTP2. They have identical 5’UTRs and only ten single nucleotide polymorphisms in the open reading frames (ORFs). However, the 3’UTRs differ dramatically in sequence and length. We found that the two TCTP mRNAs are differentially expressed duringT. bruceilife cycle. While procyclic form trypanosomes (PCF) express TCTP1, the bloodstream form trypanosomes (BSF), express TCTP2. We link the differential expression to the distinct 3’UTRs of the paralogues. In PCF cells, the protein appears to localize in the cytosol. We show that TCTP1 is essential for normal cell growth and has pleiotropic effects on the cells including aberrant cell morphology, enlarged and reduced number of acidocalcisomes and appearance of accumulations in the mitochondria.
ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data
Authors: Reynolds Stephanie , Abrahamsson Therese , Schuck Renaud , Jesper Sjöström P. , Schultz Simon R. , Dragotti Pier Luigi 
Published: September 2017

AbstractWe present an algorithm for detecting the location of cells from two-photon calcium imaging data. In our framework, multiple coupled active contours evolve, guided by a model-based cost function, to identify cell boundaries. An active contour seeks to partition a local region into two subregions, a cell interior and ex-terior, in which all pixels have maximally ‘similar’ time courses. This simple, local model allows contours to be evolved predominantly independently. When contours are sufficiently close, their evolution is coupled, in a manner that permits overlap. We illustrate the ability of the proposed method to demix overlapping cells on real data. The proposed framework is flexible, incorporating no prior information regarding a cell’s morphology or stereotypical temporal activity, which enables the detection of cells with diverse properties. We demonstrate algorithm performance on a challenging mousein vitrodataset, containing synchronously spiking cells, and a manually labelled mousein vivodataset, on which ABLE achieves a 67.5% success rate.Significance statementTwo-photon calcium imaging enables the study of brain activity during learning and behaviour at single-cell resolution. To decode neuronal spiking activity from the data, algorithms are first required to detect the location of cells in the video. It is still common for scientists to perform this task manually, as the heterogeneity in cell shape and frequency of cellular overlap impede automatic segmentation algorithms. We developed a versatile algorithm based on a popular image segmentation approach (the Level Set Method) and demonstrated its capability to overcome these challenges. We include no assumptions on cell shape or stereotypical temporal activity. This lends our framework the flexibility to be applied to new datasets with minimal adjustment.
A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State
Authors: Stynen B. , Abd-Rabbo D. , Kowarzyk J. , Miller-Fleming L. , Ralser M. , Michnick S.W. 
Published: September 2017

AbstractWe report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins or other small molecules based on “homomer dynamics” Protein-fragment Complementation Assays (hdPCA).hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions.hdPCA complements genetic interaction measurements while eliminating confounding effects of gene ablation. We demonstrate thathdPCA accurately predicts the effects of two longevity and health-span-affecting drugs, immunosuppressant rapamycin and type II diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatments of diabetes, cancers and other chronic diseases of aging.
Symbiodiniumfunctional diversity and clade specificity under global change stressors
Authors: Davies S.W. , Ries J.B. , Marchetti A , Granzotti Rafaela , Castillo K.D. 
Published: September 2017

ABSTRACTCoral bleaching episodes are increasing in frequency, demanding examination of the physiological and molecular responses of corals and theirSymbiodiniumto climate change. Here we quantify bleaching andSymbiodiniumphotosynthetic performance ofSiderastrea sidereafrom two reef zones after long-term exposure to thermal and CO2-acidification stress. Molecular response ofin hospite Symbiodiniumto these stressors was interrogated with RNAseq. Elevated temperatures reduced photosynthetic efficiency, which was highly correlated with bleaching status. However, photosynthetic efficiencies of forereef symbionts were more negatively affected by thermal stress than nearshore symbionts, indicating greater thermal tolerance in nearshore corals. At control temperatures, CO2-acidification had little effect on symbiont physiology, although forereef symbionts exhibited greater photosynthetic efficiencies than nearshore symbionts. Transcriptome profiling revealed thatS. sidereawere dominated by clade CSymbiodinium, except under thermal stress, which caused shifts to thermotolerant clade D. Comparative transcriptomics of conserved genes across symbiotic partners revealed few differentially expressedSymbiodiniumgenes when compared to corals. Instead of responding to stress, clade C transcriptomes varied by reef zone, with forereefSymbiodiniumexhibiting enrichment of genes associated with photosynthesis. Our findings suggest that functional variation in photosynthetic architecture exists between forereef and nearshoreSymbiodiniumpopulations.
Influential parameters for the analysis of intracellular parasite metabolomics
Authors: Carey Maureen A. , Covelli Vincent , Brown Audrey , Medlock Gregory L. , Haaren Mareike , Cooper Jessica G. , Papin Jason A. , Guler Jennifer L. 
Published: September 2017

ABSTRACTMetabolomics is increasingly popular for the study of many pathogens. For the malaria parasite,Plasmodium falciparum, both targeted and untargeted metabolite detection has improved our understanding of pathogenesis, host-parasite interactions, and antimalarial drug treatment and resistance. However, purification and analysis procedures for performing metabolomics on intracellular pathogens have not been explored. Here, we investigate the impact of host contamination on the metabolome when preparing samples using standard methods. We purifiedin vitrogrown ring stage intra-erythrocyticP. falciparumparasites for untargeted metabolomics studies; the small size of this developmental stage amplifies the challenges associated with metabolomics studies as the ratio between host and parasite biomass is maximized. Following metabolite identification and data preprocessing, we investigated whether host contributions could be corrected post hoc using various normalization approaches (including double stranded DNA, total protein, or parasite number). We conclude that normalization parameters have large effects on differential abundance analysis and recommend the thoughtful selection of these parameters. However, normalization does not remove the contribution from the parasite’s extracellular environment (culture media and host erythrocyte). In fact, we found that extra-parasite material is as influential on the metabolome as treatment with a potent antimalarial drug with known metabolic effects (artemisinin). Because of this influence, we could not detect significant changes associated with drug treatment. Instead, we identified metabolites predictive of host and media contamination that can be used to assess sample purification. Our findings provide a basis for development of improved experimental and analytical methods for future metabolomics studies of intracellular organisms.
Timber under real fire conditions – the influence of oxygen content and gas velocity on the charring behavior
Authors: Schmid Joachim , Santomaso Alessandro , Brandon Daniel , Wickström Ulf , Frangi Andrea 
Published: September 2017

Purpose
The purpose of this study is to investigate the influencing factors on the charring behaviour of timber, the char layer and the charring depth in non-standard fires.

Design/methodology/approach
This paper summarizes outcomes of tests, investigating the influences on the charring behavior of timber by varying the oxygen content and the gas velocity in the compartment. Results show that charring is depending on the fire compartment temperature, but results show further that at higher oxygen flow, char contraction was observed affecting the protective function of the char layer.

Findings
In particular, in the cooling phase, char contraction should be considered which may have a significant impact on performance-based design using non-standard temperature fire curves where the complete fire history including the cooling phase has to be taken into account.

Originality/value
Up to now, some research on non-standard fire exposed timber member has been performed, mainly based on standard fire resistance tests where boundary conditions as gas flow and oxygen content especially in the decay phase are not measured or documented. The approach presented in this paper is the first documented fire tests with timber documenting the data required.
Rewilded mammal assemblages reveal the missing ecological functions of granivores
Authors: Mills Charlotte H. , Gordon Christopher E. , Letnic Mike 
Published: September 2017

Abstract

Rewilding is a strategy for ecological restoration that uses reintroductions of animals to re‐establish the ecological functions of keystone species. Globally, rewilding efforts have focused primarily on reinstating the ecological functions of charismatic megafauna. In Australia, rewilding efforts have focused on restoring the ecological functions of herbivorous and omnivorous rodents and marsupials weighing between 30 and 5,000 g inside of predator‐proof exclosures.

In many arid ecosystems, mammals are considered the dominant seed predators. In Australian deserts, ants are considered to be the primary removers and predators of seeds and mammals unimportant removers and predators of seeds. However, most research on granivory in Australian deserts has occurred in areas where native mammals were functionally extinct.

Here, we compare rates of seed removal by mammals and ants on shrub seeds and abundance of shrub seedlings in two rewilded desert ecosystems (Arid Recovery Reserve and Scotia Wildlife Sanctuary) with adjacent areas possessing depauperate mammal faunas. We used foraging trays containing seeds of common native shrubs (Acacia ligulata and Dodonaea viscosa) to examine rates of seed removal by ants and mammals. We quantified the abundance of A. ligulata and D. viscosa seedlings inside and outside of rewilded areas along belt transects.

By excluding ants and mammals from foraging trays, we show that ants removed more seeds than mammals where mammal assemblages were depauperate, but mammals removed far more seeds than ants in rewilded areas. Shrub seedlings were more abundant in areas with depauperate mammal faunas than in rewilded areas.

Our study provides evidence that rewilding of desert mammal assemblages has restored the hitherto unappreciated ecological function of omnivorous rodents and bettongs as seed predators. We hypothesize that the loss of omnivorous mammals may be a factor that has facilitated shrub encroachment in arid Australia.

We contend that rewilding programs aimed at restoring ecological processes should not ignore consumers with relatively lower per capita consumptive effects. This is because consumers with low per capita consumptive effects often occur at high population densities or perform critical ecological functions and thus may have significant population level impacts that can be harnessed for ecological restoration.

A plain language summary is available for this article.
Extended reflectivity method for modelling the propagation of diffusive–viscous wave in dip‐layered media
Authors: Zhao Haixia , Gao Jinghuai , Peng Jigen 
Published: September 2017

ABSTRACTThe reflectivity method plays an important role in seismic modelling. It has been used to model different types of waves propagating in elastic and anelastic media. The diffusive–viscous wave equation was proposed to investigate the relationship between frequency dependence of reflections and fluid saturation. It is also used to describe the attenuation property of seismic wave in a fluid‐saturated medium. The attenuation of diffusive–viscous wave is mainly characterised by the effective attenuation parameters in the equation. Thus, it is essential to obtain those parameters and further characterise the features of the diffusive–viscous wave. In this work, we use inversion method to obtain the effective attenuation parameters through quality factor to investigate the characteristics of diffusive–viscous wave by comparing with those of the viscoacoustic wave. Then, the reflection/transmission coefficients in a dip plane‐layered medium are studied through coordinate transform and plane‐wave theory. Consequently, the reflectivity method is extended to compute seismograms of diffusive–viscous wave in a dip plane multi‐layered medium. Finally, we present two models to simulate the propagation of diffusive–viscous wave in a dip plane multi‐layered medium by comparing the results with those in a viscoacoustic medium. The numerical results demonstrate the validity of our extension of reflectivity method to the diffusive–viscous medium. The numerical examples in both time domain and time–frequency domain show that the reflections from a dip plane interface have significant phase shift and amplitude change compared with the results of horizontal plane interface due to the differences in reflection/transmission coefficients. Moreover, the modelling results show strong attenuation and phase shift in the diffusive–viscous wave compared to those of the viscoacoustic wave.
Strategies for stable attenuation compensation in reverse‐time migration
Authors: Sun Junzhe , Zhu Tieyuan 
Published: September 2017

ABSTRACTAttenuation in seismic wave propagation is a common cause for poor illumination of subsurface structures. Attempts to compensate for amplitude loss in seismic images by amplifying the wavefield may boost high‐frequency components, such as noise, and create undesirable imaging artefacts. In this paper, rather than amplifying the wavefield directly, we develop a stable compensation operator using stable division. The operator relies on a constant‐Q wave equation with decoupled fractional Laplacians and compensates for the full attenuation phenomena by performing wave extrapolation twice. This leads to two new imaging conditions to compensate for attenuation in reverse‐time migration. A time‐dependent imaging condition is derived by applying Q‐compensation in the frequency domain, whereas a time‐independent imaging condition is formed in the image space by calculating image normalisation weights. We demonstrate the feasibility and robustness of the proposed methods using three synthetic examples. We found that the proposed methods are capable of properly compensating for attenuation without amplifying high‐frequency noise in the data.
Patterns of Collaboration among Health Care and Social Services Providers in Communities with Lower Health Care Utilization and Costs
Authors: Brewster Amanda L. , Brault Marie A. , Tan Annabel X. , Curry Leslie A. , Bradley Elizabeth H. 
Published: September 2017

ObjectiveTo understand how health care providers and social services providers coordinate their work in communities that achieve relatively low health care utilization and costs for older adults.Study SettingSixteen Hospital Service Areas (HSAs) in the United States.Study DesignWe conducted a qualitative study of HSAs with performance in the top or bottom quartiles nationally across three key outcomes: ambulatory care sensitive hospitalizations, all‐cause risk‐standardized readmission rates, and average reimbursements per Medicare beneficiary. We selected 10 higher performing HSAs and six lower performing HSAs for inclusion in the study.Data CollectionTo understand patterns of collaboration in each community, we conducted site visits and in‐depth interviews with a total of 245 representatives of health care organizations, social service agencies, and local government bodies.Principal FindingsOrganizations in higher performing communities regularly worked together to identify challenges faced by older adults in their areas and responded through collective action—in some cases, through relatively unstructured coalitions, and in other cases, through more hierarchical configurations. Further, hospitals in higher performing communities routinely matched patients with needed social services.ConclusionsThe collaborative approaches used by higher performing communities, if spread, may be able to improve outcomes elsewhere.
Ecological characteristics of a cave‐dwelling moth species, Triphosa dubitata (Lepidoptera: Geometridae), in Baram and Ssang caves in Gangwon Province, Korea
Authors: Kim Do Sung , Park Soeng Joon , Han Sang Hoon , Choi Don Won , Choi Young Gun , Kim Hyun Jung , Kim Dong Gun , Yi Hoonbok 
Published: September 2017

AbstractThis study was performed to clarify the ecological characteristics of a cave‐dwelling moth species, Triphosa dubitata Linnaeus (Lepidoptera: Geometridae), at Baram cave and at Ssang cave within Pyeongchang‐gun of Gangwon province in south Korea. We investigated T. dubitata population for 3 days from March 2013 to October 2013 (except September) and in January 2014. We used a section investigation method in the caves every month to determine their ecological characteristic. A nocturnal investigation using a high intensity discharge lamp adjacent to the entrance of the cave was conducted in parallel with a diurnal investigation using butterfly traps to investigate the movement of T. dubitata. In order to investigate the range of habitat temperature of moths, we used a dual laser targeting infrared thermometer to measure the cave temperatures. We caught individuals of T. dubitata L.: 8,574 individuals in Baram cave and 828 individuals in Ssang cave. As 9,095 individuals (97 %) appeared at a temperature of −3°C ~ 8°C, it was verified that the adults were living at specific temperatures. In addition, T. dubitata adults were not active outside the caves; they entered the cave as soon as they developed from pupa into adults. These results showed that T. dubitata depended on food plants outside of the cave during the egg–larva–pupa stages, and they used the cave as a habitat for long‐term survival when they develop into adults.
Evaluation of Existing and Modified Wetland Equations in the SWAT Model
Authors: Ikenberry Charles D. , Crumpton William G. , Arnold Jeffrey G. , Soupir Michelle L. , Gassman Philip W. 
Published: September 2017

AbstractThe ability to accurately simulate flow and nutrient removal in treatment wetlands within an agricultural, watershed‐scale model is needed to develop effective plans for meeting nutrient reduction goals associated with protection of drinking water supplies and reduction of the Gulf of Mexico hypoxic zone. The objectives of this study were to incorporate new equations for wetland hydrology and nutrient removal in Soil and Water Assessment Tool (SWAT), compare model performance using original and improved equations, and evaluate the ramifications of errors in watershed and tile drain simulation on prediction of NO3‐N dynamics in wetlands. The modified equations produced Nash‐Sutcliffe Efficiency values of 0.88 to 0.99 for daily NO3‐N load predictions, and percent bias values generally less than 6%. However, statistical improvement over the original equations was marginal and both old and new equations provided accurate simulations. The new equations reduce the model's dependence on detailed monitoring data and hydrologic calibration. Additionally, the modified equations increase SWAT's versatility by incorporating a weir equation and an irreducible nutrient concentration and temperature coefficient. Model improvements enhance the utility of SWAT for simulating flow and nutrients in wetlands and other impoundments, although performance is limited by the accuracy of inflow and NO3‐N predictions from the contributing watershed. Editor's note: This paper is part of the featured series on SWAT Applications for Emerging Hydrologic and Water Quality Challenges. See the February 2017 issue for the introduction and background to the series.
International Trade as an Engine for Sustainable Development: The ITFC Experience in Supporting SMEs
Authors: Terai Anisse 
Published: September 2017

AbstractThis article seeks to shed some light on financing and supporting international trade with a particular focus on SMEs. The paper will look into the situation of Organisation of Islamic Cooperation (OIC) countries vis‐à‐vis international trade. Then, the role of multilateral development banks (MDBs) in supporting international trade will be expounded, while the following section will focus on the experience of ITFC as the sole MDB fully dedicated to trade. Afterwards, the article will cover SMEs’ state in today's world, and make the case of SME development through trade. Finally, a proposal for an innovative trade fund for SMEs will be put forward. The article will conclude with recommendations and proposals to reinforce and develop SMEs through trade for sustainable global social and economic prosperity.