bluuebunny/crossref_metadata_2025 huggingface dataset:
The Draft Genome ofKochia scopariaand the Mechanism of Glyphosate Resistance via Transposon-MediatedEPSPSTandem Gene Duplication
Authors: Patterson Eric L. , Saski Christopher A. , Sloan Daniel B. , Tranel Patrick J. , Westra Philip , Gaines Todd A.
Published: April 2019

Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world’s most-used herbicide. There are typically three to eightEPSPScopies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled theEPSPSlocus from a glyphosate-resistant kochia plant by sequencing a kochia bacterial artificial chromosome library. These resources helped reconstruct the history of duplication in the structurally complexEPSPSlocus and uncover the genes that are co-duplicated withEPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. We discovered a FHY3/FAR1-like mobile genetic element that is associated with the duplicatedEPSPSgene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of theEPSPSgene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.
Tumor-targeted delivery of childhood vaccine recall antigens by attenuatedListeriareduces pancreatic cancer
Authors: Selvanesan Benson Chellakkan , Chandra Dinesh , Quispe-Tintaya Wilber , Jahangir Arthee , Patel Ankur , Meena Kiran , Alves Da Silva Rodrigo Alberto , Friedman Madeline , Libutti Steven K , Yuan Ziqiang , Li Jenny , Siddiqui Sarah , Beck Amanda , Tesfa Lydia , Koba Wade , Chuy Jennifer , McAuliffe John C. , Jafari Rojin , Entenberg David , Wang Yarong , Condeelis John , DesMarais Vera , Balachandran Vinod , Zhang Xusheng , Gravekamp Claudia
Published: April 2019

Pancreatic ductal adenocarcinoma is highly metastatic, poorly immunogenic, and immune suppression prevents T cell activation in the tumor microenvironment. We developed a microbial-based immunotherapeutic concept for selective delivery of a highly immunogenic tetanus toxoid protein (TT856-1313), into tumor cells by attenuatedListeria monocytogenes, and reactivation of pre-existing TT-specific memory T cells (generated during childhood) to kill infected tumor cells. Thus, TT here functions as an alternative for neoantigens. Treatment of KPC mice withListeria-TT resulted in TT accumulation in tumors and inside tumor cells, and attraction of predominantly TT-specific memory CD4 T cells. Moreover, gemcitabine (GEM) combined withListeria-TTsignificantly improved the migration of CD4 T cells into tumors and the production of perforin and granzyme B, turning cold tumors into immunological hot tumors.In vivodepletion of T cells in Listeria-TT+GEM-treated mice demonstrated CD4 T cell-mediated eradication of tumors and metastases (Mann-Whitney p<0.05). In addition, peritumoral lymph node like structures (LNS) were observed in close contact with the pancreatic tumors displaying CD4 T cells and CD8 T cells of KPC mice treated withListeria-TT orListeria-TT+GEM. The production of perforin and granzyme B was observed in LNS of KPC mice that receivedListeria-TT+GEM. This combination not only reduced tumor burden (80%) and metastases (87%) significantly (p<0.05, Mann-Whitney), but also improved the survival time of KPC mice with advanced pancreatic cancer substantially (Mantel-Cox p<0.0001). Our results unveil new mechanisms ofListeriaand GEM improving immunotherapy for PDAC.
A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer
Authors: Lee Brian H. , Kelly Geoffrey , Bradford Shermineh , Davila Melanie , Guo Xinzheng V. , Amir El-ad David , Thrash Emily M. , Solga Michael D. , Lannigan Joanne , Sellers Brian , Candia Julian , Tsang John , Montgomery Ruth R. , Tamaki Stanley J. , Sigdel Tara K. , Sarwal Minnie M. , Lanier Lewis L. , Tian Yuan , Kim Cheryl , Hinz Denise , Peters Bjoern , Sette Alessandro , Rahman Adeeb H.
Published: April 2019

Mass cytometry is a powerful tool for high dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. Fluidigm’s 3rd-generation Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median signal intensities and higher coefficients of variation in antibody expression. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multi-site study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces inter-instrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multi-center studies.
Loss of Ku’s DNA end binding activity affects telomere length via destabilizing telomere-bound Est1 rather than altering TLC1 homeostasis
Authors: Lemon Laramie D. , Morris Danna K. , Bertuch Alison A.
Published: April 2019

Saccharomyces cerevisiaetelomerase, which maintains telomere length, is comprised of an RNA component, TLC1, the reverse transcriptase, Est2, and regulatory subunits, including Est1. The Yku70/Yku80 (Ku) heterodimer, a DNA end binding (DEB) protein, also contributes to telomere length maintenance. Ku binds TLC1 and telomere ends in a mutually exclusive fashion, and is required to maintain levels and nuclear localization of TLC1. Ku also interacts with Sir4, which localizes to telomeres. Here we sought to determine the role of Ku’s DEB activity in telomere length maintenance by utilizingyku70-R456Emutant strains, in which Ku has reduced DEB and telomere association but proficiency in TLC1 and Sir4 binding, and TLC1 nuclear retention. Telomere lengths in ayku70-R456Estrain were nearly as short as those inykuΔstrains and shorter than in strains lacking either Sir4, Ku:Sir4 interaction, or Ku:TLC1 interaction. TLC1 levels were decreased in theyku70-R456Emutant, yet overexpression of TLC1 failed to restore telomere length. Reduced DEB activity did not impact Est1’s ability to associate with telomerase but did result in decreased association of Est1 with the telomere. These findings suggest Ku’s DEB activity maintains telomere length homeostasis by preserving Est1’s interaction at the telomere rather than altering TLC1 levels.
DeeplyTough: Learning Structural Comparison of Protein Binding Sites
Authors: Simonovsky Martin , Meyers Joshua
Published: April 2019

Motivation

Protein binding site comparison (pocket matching) is of importance in drug discovery. Identification of similar binding sites can help guide efforts for hit finding, understanding polypharmacology and characterization of protein function. The design of pocket matching methods has traditionally involved much intuition, and has employed a broad variety of algorithms and representations of the input protein structures. We regard the high heterogeneity of past work and the recent availability of large-scale benchmarks as an indicator that a data-driven approach may provide a new perspective.

Results

We propose DeeplyTough, a convolutional neural network that encodes a three-dimensional representation of protein binding sites into descriptor vectors that may be compared efficiently in an alignment-free manner by computing pairwise Euclidean distances. The network is trained with supervision: (i) to provide similar pockets with similar descriptors, (ii) to separate the descriptors of dissimilar pockets by a minimum margin, and (iii) to achieve robustness to nuisance variations. We evaluate our method using three large-scale benchmark datasets, on which it demonstrates excellent performance for held-out data coming from the training distribution and competitive performance when the trained network is required to generalize to datasets constructed independently.

Availability

https://github.com/BenevolentAI/DeeplyTough

Contact

martin.simonovsky@enpc.fr,joshua.meyers@benevolent.ai
Separate domains of G3BP promote efficient clustering of alphavirus replication complexes and recruitment of the translation initiation machinery
Authors: Götte Benjamin , Panas Marc D , Hellström Kirsi , Liu Lifeng , Samreen Baila , Larsson Ola , Ahola Tero , McInerney Gerald M
Published: April 2019

G3BP-1 and -2 (hereafter referred to as G3BP) are multifunctional RNA-binding proteins involved in stress granule (SG) assembly. Viruses from diverse families target G3BP for recruitment to replication or transcription complexes in order to block SG assembly but also to acquire pro-viral effects via other unknown functions of G3BP. The Old World alphaviruses, including Semliki Forest virus (SFV) and chikungunya virus (CHIKV) recruit G3BP into viral replication complexes, via an interaction between FGDF motifs in the C-terminus of the viral non-structural protein 3 (nsP3) and the NTF2-like domain of G3BP. To study potential proviral roles of G3BP, we used human osteosarcoma (U2OS) cell lines lacking endogenous G3BP generated using CRISPR-Cas9 and reconstituted with a panel of G3BP1 mutants and truncation variants. While SFV replicated with varying efficiency in all cell lines, CHIKV could only replicate in cells expressing G3BP1 variants containing both the NTF2-like and the RGG domains. The ability of SFV to replicate in the absence of G3BP allowed us to study effects of different domains of the protein. We used immunoprecipitation to demonstrate that that both NTF2- like and RGG domains are necessary for the formation a complex between nsP3, G3BP1 and the 40S ribosomal subunit. Electron microscopy of SFV-infected cells revealed that formation of nsP3:G3BP1 complexes via the NTF2-like domain was necessary for clustering of cytopathic vacuoles (CPVs) and that the presence of the RGG domain was necessary for accumulation of electron dense material containing G3BP1 and nsP3 surrounding the CPV clusters. Clustered CPVs also exhibited localised high levels of translation of viral mRNAs as detected by ribopuromycylation staining. These data confirm that G3BP is a ribosomal binding protein and reveal that alphaviral nsP3 uses G3BP to concentrate viral replication complexes and to recruit the translation initiation machinery, promoting the efficient translation of viral mRNAs.
ERASE: Extended Randomization for assessment of annotation enrichment in ASE datasets
Authors: D’Sa Karishma , Reynolds Regina H. , Guelfi Sebastian , Zhang David , Ruiz Sonia Garcia ,   International Parkinson’s Disease Genomics Consortium (IPDGC),   System Genomics of Parkinson’s Disease (SGPD), Hardy John , Gagliano Taliun Sarah A. , Small Kerrin S. , Ryten Mina , Botía Juan A.
Published: April 2019

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with various human phenotypes and many of these loci are thought to act at a molecular level by regulating gene expression. Detection of allele specific expression (ASE), namely preferential usage of an allele at a transcribed locus, is an increasingly important means of studying the genetic regulation of gene expression. However, there are currently a paucity of tools available to link ASE sites with GWAS risk loci. Existing integration methods first use ASE sites to infer cis-acting expression quantitative trait loci (eQTL) and then apply eQTL-based approaches. ERASE is a method that assesses the enrichment of risk loci amongst ASE sites directly. Furthermore, ERASE enables additional biological insights to be made through the addition of other SNP level annotations. ERASE is based on a randomization approach and controls for read depth, a significant confounder in ASE analyses. In this paper, we demonstrate that ERASE can efficiently detect the enrichment of eQTLs and risk loci within ASE data and that it remains sensitive even when used with underpowered GWAS datasets. Finally, using ERASE in combination with GWAS data for Parkinson’s disease and data on the splicing potential of individual SNPs, we provide evidence to suggest that risk loci for Parkinson’s disease are enriched amongst ASEs likely to affect splicing. Thus, we show that ERASE is an important new tool for the integration of ASE and GWAS data, capable of providing novel insights into the pathophysiology of complex diseases.
The Role of CD147 in Leukocyte Aggregation in Liver Injury
Authors: Yee Christine , Main Nathan , Terry Alexandra , Stevanovski Igor , Maczurek Annette , Morgan Alison J. , Calabro Sarah , Potter Alison J. , Iemma Tina L. , Bowen David G. , Ahlenstiel Golo , Warner Fiona J. , McCaughan Geoffrey W. , McLennan Susan V. , Shackel Nicholas A.
Published: April 2019

Background

Chronic inflammation is the driver of liver injury resulting in progressive fibrosis and eventual cirrhosis. The consequences include both liver failure and liver cancer. We have previously described increased expression of the highly multifunctional glycoprotein CD147 in liver injury. This work describes a novel role of CD147 in liver inflammation and the importance of leukocyte aggregates in determining the extent of liver injury.

Methods

Non-diseased, progressive injury and cirrhotic liver from humans and mice were examined using mAb targeting CD147. Inflammatory cell subsets were assessed by multicolor flow cytometry.

Results

In liver injury, we observe abundant intrahepatic leukocyte clusters defined as ≥5 adjacent CD45+cells which we have labelled “leukocyte aggregates”. We have shown that these leukocyte aggregates are significant in determining the extent of liver injury. If CD147 is blockedin vivo,these leukocyte aggregates diminish in size and number together with a marked significant reduction in liver injury including fibrosis. This accompanied by no change in overall intrahepatic leukocyte numbers. Further, blocking aggregation formation occurs prior to an appreciable increase in inflammatory markers or fibrosis. Additionally, there were no observed, “off-target” or unpredicted effects in targeting CD147.

Conclusion

CD147 mediates leukocyte aggregation which is associated with the development of liver injury. This is not a secondary effect, but a cause of injury as aggregate formation proceeds other markers of injury. Leukocyte aggregation has been previously described in inflammation dating back over many decades but till now been shown to determine the extent of injury.
Isolation of persisters enabled by ß-lactam-induced filamentation reveals their single-cell awakening characteristics
Authors: Windels Etthel M. , Meriem Zacchari Ben , Zahir Taiyeb , Verstrepen Kevin J. , Hersen Pascal , Van den Bergh Bram , Michiels Jan
Published: April 2019

When exposed to lethal doses of antibiotics, bacterial populations are most often not completely eradicated. A small number of phenotypic variants, defined as ‘persisters’, are refractory to antibiotics and survive treatment. Despite their involvement in relapsing infections caused by major pathogens, processes determining phenotypic switches from and to the persister state largely remain elusive. This is mainly due to the low frequency of persisters in a population and the lack of reliable persistence markers, both hampering studies of persistence at the single-cell level. Problematically, existing methods to enrich for persisters result in samples with very low persister densities and/or a too high abundance of other cell types. Here we present a novel and highly effective persister isolation method involving cephalexin, an antibiotic that induces extensive filamentation of susceptible cells. We show that antibiotic-tolerant cells can easily be separated by size after a short cephalexin treatment, and that the isolated cells are genuine persisters. We used our isolation method to monitor persister outgrowth at the single-cell level in a microfluidic device, thereby conclusively demonstrating that awakening is a stochastic phenomenon. We anticipate that our novel approach can have far-reaching consequences in the persistence field, by allowing single-cell studies at a much higher throughput than previously reported.
Optical induction of autophagy viaTranscription factor EB(TFEB) reduces pathological tau in neurons
Authors: Binder JL , Deretic V , Weick JP , Bhaskar K
Published: April 2019

Aggregation and accumulation of microtubule associated protein tau in neurons is major neuropathological hallmark of Alzheimer’s disease (AD) and related tauopathies. Attempts have been made to promote clearance of pathological tau (p-Tau) from neurons via autophagy. Over expression of transcription factor EB (TFEB), has shown to clear pTau from neurons via autophagy. However, sustained TFEB activation and/or autophagy can create burden on cellular bioenergetics and can be deleterious. Thus, we engineered a minimally invasive optical system that could transiently alter autophagic flux. We optimized and tested an optogenetic gene expression system derived from a previously engineered bacterial transcription factor, EL222. For the first time, our group utilized this system not only to spatial-temporally control nuclear TFEB expression, we also show light-induced TFEB has the capacity to reduce p-Tau burden in AD patient-derived human iPSC-neurons. Together, these results suggest that optically-regulatable gene expression of TFEB unlocks opto-therapeutics to treat AD and other dementias.
Apoptosis in the fetal testis eliminates developmentally defective germ cell clones
Authors: Nguyen Daniel H. , Laird Diana J.
Published: April 2019

Many germ cells (GCs) are eliminated during development, long before differentiating to egg or sperm, but it is not clear why. Here, we examined how GC composition in the mouse fetal testis is altered by scheduled apoptosis during sex differentiation. Multicolored-lineage tracing revealed that apoptosis affects clonally-related GCs, suggesting that this fate decision occurs autonomously based on shared intrinsic properties. We identified extensive transcriptional heterogeneity among fetal GCs including an apoptosis-susceptible subpopulation delineated by high Trp53 and deviant differentiation. Alternatively, the GC subpopulation most likely to survive was advanced in differentiation. These results indicate that GC developmental fate is based upon discrete and cell-heritable fitnesses and imply that a dichotomy between sex-differentiation and apoptosis coordinates the removal of developmentally incompetent cells to improve gamete quality. Evidence that GC subpopulations are in different epigenetic states suggests that errors in epigenetic reprogramming form the basis of aberrant differentiation and apoptotic selection.

One sentence summary

Germ cells undergo autonomous selection in the fetal testis to promote male differentiation
CNTNAP2 is targeted to endosomes by the polarity protein Par3
Authors: Gao Ruoqi , Pratt Christopher P. , Yoon Sehyoun , Martin-de-Saavedra Maria Dolores , Forrest Marc P. , Penzes Peter
Published: April 2019

A decade of genetic studies has established Contactin-associated protein-like 2 (CNTNAP2) as a prominent susceptibility gene associated with multiple neurodevelopmental disorders. The development and characterization of Cntnap2 knockout models in multiple species have bolstered this claim by establishing clear connections with certain endophenotypes. Despite these remarkable in vivo findings, CNTNAP2’s molecular functions are relatively unexplored, highlighting the need to identify novel protein partners. Here, we characterized an interaction between CNTNAP2 and Partitioning-defective 3 (Par3) – a polarity molecule we isolated in a yeast-two hybrid screen with CNTNAP2’s C-terminus. We provide evidence that the two proteins interact via PDZ domain-mediated binding, that CNTNAP2+/Par3+ complexes are largely associated with clathrin-coated endocytic vesicles, and that Par3 causes an enlargement of these structures. Live imaging and fluorescence recovery after photobleaching (FRAP) reveals that Par3 limits the mobility of CNTNAP2 at endosomes, thus stabilizing it at that location. Finally, expression of Par3 but not Par3ΔPDZ can cluster endogenous CNTNAP2 in primary neurons. Collectively, we conclude that Par3 regulates CNTNAP2 spatial localization to endocytic compartments.
Direct migration of ambient seismic data
Authors: Girard Aaron J. , Shragge Jeffrey
Published: April 2019

Utilising ambient seismic energy naturally propagating in the Earth as an alternative approach to active body‐wave seismic investigations has been a topic of interest for a number of decades. However, because ambient surface‐wave arrivals typically are of much greater amplitude than ambient body‐wave energy, significant data signal processing and long recording times are required to mitigate this and other coherent noise sources, and to correlate sufficient reflected body‐wave energy to converge to a stable image. Even for these scenarios, identifying and validating imaged body‐wave reflection events remain challenging. In active‐source investigations, extended imaging condition gathers are used to examine velocity (in)accuracy. Herein, we develop an ambient direct migration approach that uses a novel ambient (deconvolution) extended imaging condition. We simulate synthetic ambient‐wavefield seismic data for two different models and use a field data set from Lalor Lake in Manitoba, Canada, to conduct a series of numerical experiments to demonstrate the velocity sensitivity and long‐term stationarity of ambient‐wavefield seismic data in the migration image domain. Tests with varying global velocity perturbations show a characteristic reflector moveout in deconvolution extended imaging condition gathers that can serve as a diagnostic of reflected ambient body‐wave energy. We illustrate that this imaging formalism, under idealised circumstances, gives comparable results to conventional seismic methods, which extends the use of extended imaging condition gather‐based image validation to ambient‐wavefield seismic data scenarios. We assert that this may be a valuable tool for the validation of ambient migration techniques that to date have yielded largely inconclusive results.
A hybrid optimization scheme for self‐potential measurements due to multiple sheet‐like bodies in arbitrary 2D resistivity distributions
Authors: Giannakis Iraklis , Tsourlos Panagiotis , Papazachos Costas , Vargemezis George , Giannopoulos Antonios , Papadopoulos Nikos , Tosti Fabio , Alani Amir
Published: April 2019

Self‐potential is a passive geophysical method that can be applied in a straightforward manner with minimum requirements in the field. Nonetheless, interpretation of self‐potential data is particularly challenging due to the inherited non‐uniqueness present in all potential methods. Incorporating information regarding the target of interest can facilitate interpretation and increase the reliability of the final output. In the current paper, a novel method for detecting multiple sheet‐like targets is presented. A numerical framework is initially described that simulates sheet‐like bodies in an arbitrary 2D resistivity distribution. A scattered field formulation based on finite differences is employed that allows the edges of the sheet to be independent of the grid geometry. A novel analytical solution for two‐layered models is derived and subsequently used to validate the accuracy of the proposed numerical scheme. Lastly, a hybrid optimization is proposed that couples linear least‐squares with particle‐swarm optimization in order to effectively locate the edges of multiple sheet‐like bodies. Through numerical and real data, it is proven that the hybrid optimization overcomes local minimal that occurs in complex resistivity distributions and converges substantially faster compared to traditional particle‐swarm optimization.
Top‐down effects of repatriating bald eagles hinder jointly recovering competitors
Authors: Cruz Jennyffer , Windels Steve K. , Thogmartin Wayne E. , Crimmins Shawn M. , Grim Leland H. , Larson James H. , Zuckerberg Benjamin
Published: April 2019

The recovery of piscivorous birds around the world is touted as one of the great conservation successes of the 21st century, but for some species, this success was short‐lived. Bald eagles, ospreys and great blue herons began repatriating Voyageurs National Park, USA, in the mid‐20th century. However, after 1990, only eagles continued their recovery, while osprey and heron recovery failed for unknown reasons.

We aimed to evaluate whether top‐down effects of bald eagles and bottom‐up effects of inclement weather, habitat quality and fish resources contributed to the failed recovery of ospreys and herons in a protected area.

We quantified the relative influence of top‐down and bottom‐up factors on nest colonization, persistence (i.e., nest reuse) and success for ospreys, and occurrence and size of heronries using 26 years (1986–2012) of spatially explicit monitoring data coupled with multi‐response hierarchical models and Bayesian variable selection approaches.

Bald eagles were previously shown to recover faster due to intensive nest protection and management. Increased numbers of eagles were associated with a reduction in the numbers of osprey nests, their nesting success and heronry size, while higher local densities of nesting eagles deterred heronries nearby. We found little evidence of bottom‐up limitations on the failed recovery of herons and ospreys.

We present a conservation conundrum: bald eagles are top predators and a flagship species of conservation that have benefited from intensive protection, but this likely hindered the recovery of ospreys and herons. Returning top predators, or rewilding, is widely promoted as a conservation strategy for top‐down ecosystem recovery, but managing top predators in isolation of jointly recovering species can halt or reverse ecosystem recovery. Previous studies warn of the potential consequences of ignoring biotic interactions amongst recovering species, but we go further by quantifying how these interactions contributed to failed recoveries via impacts on the nesting demography of jointly recovering species. Multi‐species management is paramount to realizing the ecosystem benefits of top predator recovery.
Native forage mediates influence of irrigated agriculture on migratory behaviour of elk
Authors: Barker Kristin J. , Mitchell Michael S. , Proffitt Kelly M.
Published: April 2019

Ungulates migrate to maximize nutritional intake when forage varies seasonally. Populations of ungulates often include both migratory and non‐migratory individuals, but the mechanisms driving individual differences in migratory behaviour are not well‐understood.

We quantified associations between hypothesized drivers of partial migration and the likelihood of migration for individual ungulates that experienced a range of environmental conditions and anthropogenic influences.

We evaluated the effects of forage variation, conspecific density, and human land uses on migratory behaviour of 308 adult female elk in 16 herds across western Montana.

We found irrigated agriculture on an individual's winter range reduced migratory behaviour, but individuals were more likely to migrate away from irrigated agricultural areas if better forage was available elsewhere or if they experienced high conspecific density on their winter range. When the forage available during the summer growing season varied predictably between years, elk were more likely to migrate regardless of whether they had access to irrigated agriculture.

Our study shows that predictable availability of beneficial native forage can encourage migration even for ungulates with irrigated agriculture on their winter range. Perturbations that can affect the forage available to ungulates include wildfires, timber harvest, livestock grazing and changing weather patterns. If these or other disturbances negatively affect forage on summer ranges of migrants, or if they cause forage to vary unpredictably across space and time, our results suggest migratory behaviour may decline as a result.
Plant functional trait shifts explain concurrent changes in the structure and function of grassland soil microbial communities
Authors: Boeddinghaus Runa S. , Marhan Sven , Berner Doreen , Boch Steffen , Fischer Markus , Hölzel Norbert , Kattge Jens , Klaus Valentin H. , Kleinebecker Till , Oelmann Yvonne , Prati Daniel , Schäfer Deborah , Schöning Ingo , Schrumpf Marion , Sorkau Elisabeth , Kandeler Ellen , Manning Peter
Published: April 2019

Land‐use intensification drives changes in microbial communities and the soil functions they regulate, but the mechanisms underlying these changes are poorly understood as land use can affect soil communities both directly (e.g. via changes in soil fertility) and indirectly (e.g. via changes in plant inputs).

The speed of microbial responses is also poorly understood. For instance, whether it is long‐term legacies or short‐term changes in land‐use intensity that drive changes in microbial communities.

To address these topics, we measured multiple microbial functions, bacterial and fungal biomass and abiotic soil properties at two time intervals 3 years apart. This was performed in 150 grassland sites differing greatly in management intensity across three German regions.

Observed changes in microbial soil properties were related to both long‐term means and short‐term changes in: abiotic soil properties, land‐use intensity, community abundance‐weighted means of plant functional traits and plant biomass properties in regression and structural equation models. Plant traits, particularly leaf phosphorus, and soil pH were the best predictors of change in soil microbial function, as well as fungal and bacterial biomass, while land‐use intensity showed weaker effects.

Indirect legacy effects, in which microbial change was explained by the effects of long‐term land‐use intensity on plant traits, were important, thus indicating a time lag between plant community and microbial change. Whenever the effects of short‐term changes in land‐use intensity were present, they acted directly on soil microorganisms.

Synthesis. The results provide new evidence that soil communities and their functioning respond to short‐term changes in land‐use intensity, but that both rapid and longer time‐scale responses to changes in plant functional traits are at least of equal importance. This suggests that management which shapes plant communities may be an effective means of managing soil communities and the functions and services they provide.
Trait identity and functional diversity co‐drive response of ecosystem productivity to nitrogen enrichment
Authors: Zhang Dianye , Peng Yunfeng , Li Fei , Yang Guibiao , Wang Jun , Yu Jianchun , Zhou Guoying , Yang Yuanhe
Published: April 2019

Exploring the mechanisms underlying the change in ecosystem productivity under anthropogenic nitrogen (N) inputs is of fundamental ecological interest. It has been proposed that functional traits, environmental factors and species richness are central drivers linking ecosystem productivity with environmental change. However, few studies have considered the joint effects of functional traits, environmental factors and species richness on ecosystem productivity under increasing N inputs.

We established a N‐manipulation experiment in a Tibetan alpine steppe in 2013. Using structural equation models, we assessed the effects of N‐induced changes in environmental factors, species richness and trait metrics (mean, variance, skewness and kurtosis of trait distribution) on gross ecosystem productivity as well as three resource use efficiencies (water, light and phosphorus (P) use efficiencies), based on measurements during the peak growing season in 2016.

We found that both light and P use efficiencies decreased under N enrichment, largely due to the N‐induced decline in functional diversity of leaf P concentration. However, both gross ecosystem productivity and water use efficiency exhibited initial increases and subsequent slight decreases with N addition. These nonlinear patterns were closely associated with both the increased morphological trait (i.e. mean of leaf area) and decreased diversity of leaf P concentration.

Synthesis. Our results illustrate how N‐induced changes in functional traits may have dual effects on ecosystem productivity: the stimulating effects of the dominant trait identity via increasing canopy light interception versus the inhibiting effect of decreasing trait diversity via declining resource use efficiencies. Our results highlight the importance of including functional traits in land surface models to improve predictions of the response of ecosystem function to N inputs.
Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon‐degrading bacterium Alcanivorax borkumensis SK2T
Authors: Gregson Benjamin H. , Metodieva Gergana , Metodiev Metodi V. , McKew Boyd A.
Published: April 2019

Alcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n‐C14) or branched (pristane) alkanes. During growth on n‐C14, A. borkumensis expressed a complete pathway for the terminal oxidation of n‐alkanes to their corresponding acyl‐CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β‐oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β‐oxidation proteins to overcome steric hinderance from branched substrates.
Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed
Authors: Molina Lázaro , Rosa Ruggero La , Nogales Juan , Rojo Fernando
Published: April 2019

Pseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.
Measuring School Efficiency and Effectiveness to Inform the Design of a School Funding Formula
Authors: Gort William , King Rebecca , Weiss Alan
Published: April 2019

In this paper, we discuss a number of key methodological and data issues presented to researchers in determining base funding requirements for Australian schools. In particular, we outline the commonly used ‘reference school’‐ based approach to determining a benchmark level of school effectiveness and efficiency, and discuss some of its limitations. In contrast to this method, we present a new approach to estimating base funding requirements that, aided by the use of more granular data, provides a more robust approach to understanding and measuring school effectiveness and efficiency.
Understanding Heterogeneous Consumer Preferences in Chinese Milk Markets: A Latent Class Approach
Authors: Wu Xiang , Hu Bin , Xiong Jie
Published: April 2019

We examine heterogeneous consumer preferences in Chinese milk markets. Using a discrete choice experiment, we examine how the brand, quality certification, traceability label and price influence consumers' milk choices. We identify four consumer segments using a latent class model: price conscious (9.8%), balanced thinking (19.8%), health conscious (57.5%), and environment conscious (12.9%) consumers. These four segments have distinct preferences: price conscious consumers prefer green certification; balanced thinking consumers have the highest willingness to pay for traceability labels; health conscious consumers have strong brand awareness; and environment conscious consumers prefer organic certification and traceability labels and use price as a quality signal. Such diversity of consumer preference can be explained by four psychological factors: price consciousness, food safety concerns, health consciousness and environmental concerns.
Visual analog scale rating change cut‐offs for detection of improvement in nausea severity
Authors: Meek Robert , Graudins Andis
Published: April 2019

Objective

To determine accuracy and best cut‐point of measured and percentage visual analog scale (VAS) change for detection of symptom improvement.

Methods

A pooled analysis of three previously published studies was conducted. All patients had baseline and 30 min VAS ratings linked to described symptom change. A receiver operating characteristic curve analysis was performed.

Results

Area under the curve for detecting symptom improvement was 0.86 (95% CI 0.83–0.90) and 0.87 (95% CI 0.84–0.90) for measured and percentage VAS change. Best cut‐points were −8 mm and −20%.

Conclusion

Accuracy of VAS change for detection of symptom improvement is good to excellent. Use of this outcome measure in future ED antiemetic trials is supported.
Effect of Blood Pump Flow and Arteriovenous Fistula Blood Flow on the Blood Pressure and Cardiac Function in Patients Undergoing Maintenance Hemodialysis
Authors: Tang Chun‐Yuan , Zhu Chun‐Ping , Wang Rao‐Ping , Ye Xiao‐Qing , Chen Xiao‐Fan , Feng Wan‐Na , Li Ping
Published: April 2019

The effect of blood pump flow rate on the cardiac functions of hemodialysis patients with arteriovenous fistula (AVF) is largely unknown. This study aimed to investigate if blood pump flow rate (Qb) and AVF access flow rate (Qa) can affect the cardiac function of Chinese hemodialysis patients. A total of 72 patients undergoing AVF hemodialysis were included from March 2010 to June 2014 and dichotomized into the high‐ and low‐flow groups using the medians of Qb (220 mL/min) and Qa (1000 mL/min) as the cutoffs. The cardiac function parameters were measured by ultrasound dilution technique within the first (t + 30) and the last (t − 30) 30 min of dialysis. At t + 30, Qb‐high group had significantly higher systolic blood pressure (SBP) and mean arterial pressure (MAP) than Qb‐low group. At t − 30, Qb‐high group had higher SBP, diastolic blood pressure (DBP), and MAP than Qb‐low group. Qa‐high group had higher SBP, MAP, cardiac output (CO), cardiac index (CI), central blood volume (CBV), and lower peripheral resistance than Qa‐low group. Multiple linear regression showed that at t − 30, Qb was positively correlated with SBP and MAP. Qa was positively correlated with CO, CI, CBV, and PR but negatively correlated with heart rate. Although Qb > 220 mL/min and Qa >1000 mL/min would elevate some parameters, the means of SBP, DBP, MAP remain within the normal range, indicating that appropriate increase in blood pump flow rate has little effect on the cardiac function of hemodialysis patients.
A ‘Most Interesting Subject for the Investigation of the Philosopher’: Conjectural History in John Barrow's Travels in China
Authors: Choi Ja Yun
Published: April 2019

This article re‐examines John Barrow's Travels in China (1804), an account of the Macartney embassy seen as having contributed to the emergence of Britain's derogatory attitude to China. By drawing connections between his cross‐cultural comparisons and conjectural history, it demonstrates how Barrow employs China's cultural differences not only to sophisticate stadial theory but also to present a complex view of Chinese civilisation that does not lend itself to an evaluative judgement of superiority. Through a comparison of Barrow's travelogue and other contemporary writings, it aims to show that British opinion on China continued to fluctuate in the early nineteenth century.
Prostate MRI evolution in clinical practice: Audit of tumour detection and staging versus prostatectomy with staged introduction of multiparametric MRI and Prostate Imaging Reporting and Data System v2 reporting
Authors: Raeside Mitchell , Low Andrew , Cohen Penelope , Sutherland Peter , Gormly Kirsten
Published: April 2019

Introduction

We conducted a retrospective audit to compare dominant nodule detection and local staging before and after the introduction of functional sequences and PI‐RADS v2 reporting to MRI prostate scans in routine private practice.

Methods

A retrospective audit was performed of 245 patients in four separate groups undergoing robotic prostatectomy for prostate cancer by a single urologist between 2009 and 2017. The initial 100 consecutive patients had T2 imaging only. The next 43 patients had T2 and DWI. 52 subsequent patients had T2, DWI and DCE sequences (mpMRI). A final 50 consecutive patients had mpMRI using PI‐RADS v2 reporting. Preoperative MRI reports were compared with prostatectomy histopathology to determine the sensitivity of MRI in detecting dominant tumour nodule and T3 extension.

Results

The addition of DWI and DCE sequences improved sensitivity for detection of dominant tumour nodule, with a significant further increase using PI‐RADS v2 reporting (38% for T2 vs. 62% for T2/DWI vs. 67% for mpMRI vs 91% for PI‐RADS v2). The accuracy of detecting T3 disease was initially very low. The use of additional imaging techniques did not significantly influence this, but the use of a three category likelihood of extraprostatic extension in the PI‐RADS v2 group had a significant increase in detection of T3 disease (sensitivity 27% vs. 23% vs. 38% vs 63%).

Conclusion

This audit tracks the significant improvements in MRI detection of prostate cancer dominant tumour nodule and T3 extension in patients undergoing prostatectomy with changing techniques and reporting standards in routine clinical practice.
Contour variation is a primary source of error when delivering post prostatectomy radiotherapy: Results of the Trans‐Tasman Radiation Oncology Group 08.03 Radiotherapy Adjuvant Versus Early Salvage (RAVES) benchmarking exercise
Authors: Cloak Kirrily , Jameson Michael G , Paneghel Andrea , Wiltshire Kirsty , Kneebone Andrew , Pearse Maria , Sidhom Mark , Tang Colin , Fraser‐Browne Carol , Holloway Lois C , Haworth Annette
Published: April 2019

Introduction

Variation in target volume delineation from clinical trial protocols has been shown to contribute to poorer patient outcomes. A clinical trial quality assurance framework can support compliance with trial protocol. Results of the TROG 08.03 RAVES benchmarking exercise considering variation from protocol, inter‐observer variability and impact on dosimetry are reported in this paper.

Methods

Clinicians were required to contour and plan a benchmarking case according to trial protocol. Geometric pjmirometers including volume, Hausdorff Distance, Mean Distance to Agreement and DICE similarity coefficient were analysed for targets and organs at risk. Submitted volumes were compared to a STAPLE and consensus ‘reference’ volume for each structure. Dosimetric analysis was performed using dose volume histogram data.

Results

Benchmarking exercise submissions were received from 96 clinicians. In total 205 protocol variations were identified. The most common variation was inadequate contouring of the CTV in 84/205 (41%). The CTV volume ranged from 65.3 to 193.1 cm3 with a median of 113.2 cm3. The most common dosimetric protocol variation related to rectal dosimetry. The mean submitted rectal volume receiving 40 Gy and 60 Gy, respectively, was 56.14% ± 5.55% and 30.25% ± 6.15%. When corrected to the protocol defined length the mean rectal volume receiving 40 Gy was 60.8% ± 7.92%, while the volume receiving 60 Gy was 33.86% ± 8.21%.

Conclusion

Variations from protocol were found in the RAVES benchmarking exercise, most notably in CTV and rectum delineation. Inter‐observer variability was evident. Incorrect delineation of the rectum impacted on dosimetric compliance with protocol.
Comparison of a combination of chemotherapy and immune checkpoint inhibitors and immune checkpoint inhibitors alone for the treatment of advanced and metastatic non‐small cell lung cancer
Authors: Kuo Chih‐Hsi Scott , Wang Chin‐Chou , Huang Yu‐Chen , Pavlidis Stelios , Liu Chien‐Ying , Ko How‐Wen , Chung Fu‐Tsai , Lin Tin‐Yu , Wang Chih‐Liang , Guo Yi‐Ke , Yang Cheng‐Ta
Published: April 2019

Background

Single agent immune checkpoint inhibitors (ICIs) improve survival outcomes compared to chemotherapy for advanced non‐small cell lung cancer (NSCLC), but treatment efficacy widely varies. The combination of ICIs with chemotherapy has shown promising efficacy over chemotherapy alone; however, whether this strategy is superior to single agent ICIs for the treatment of advanced NSCLC remains unknown.

Methods

The records of 109 patients with advanced NSCLC who were administered at least one cycle of ICIs were retrospectively reviewed. Patients were grouped based on the presence or absence of a chemotherapy treatment combination. Efficacy and survival outcomes were analyzed.

Result

Sixty‐nine (58.0%) patients received single agent ICIs (ICI group) and 50 (42.0%) received ICIs and chemotherapy (ICC group). The median (3.2 vs. 3.0 months; P = 0.025) and one‐year (34.5 vs. 9.6%; P = 0.026) progression‐free survival (PFS) rates were significantly better in the ICC than in the ICI group. The superior efficacy of ICC remained in the propensity score matched pairs (median PFS 3.2 vs. 2.6 months, P = 0.032; 1‐year PFS 35.2 vs. 7.6%; P = 0.035). Eastern Cooperative Oncology Group performance status 0–1 (HR 0.37, 95% CI 0.22–0.62; P < 0.001) and the ICC group (HR 0.56, 95% CI 0.34–0.94; P = 0.028) were predictive of PFS. Subgroup‐to‐chemotherapy interaction revealed improved risk reduction for adenocarcinoma and EGFR mutation.

Conclusion

Combing chemotherapy with ICIs improved treatment efficacy over ICIs alone. The additional efficacy of chemotherapy may differ between histological subtypes and EGFR mutation status.