bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase transformations and microstructural evolution of nanocrystalline Ti-18Zr-5Nb-3Sn-4Ta powders through mechanical alloying
Authors: Dercz Grzegorz , Matuła Izabela , Zubko Maciej , Barczyk Jagoda 
Published: February 2019

The aims of the present study are to determine the possibility of obtaining a new, nanocrystalline Ti-18Zr-5Nb-3Sn-4Ta at.-% alloy by a ball milling method, and to observe the influence of various milling times on phase composition and structure of the obtained material. The X-ray diffraction results confirmed the alloy synthesis and revealed the presence of α- and β-Ti phases. The Rietveld refinement showed that the production method and the atomic radii of the elements used in the mechanical synthesis have influence on the structure. Scanning electron microscopy observation leads to the conclusion that the powder particles and the degree of aggregation change with increasing milling time. This paper is part of a Thematic Issue on The Crystallographic Aspects of Metallic Alloys.
Unprompted vigorous physical activity is associated with higher levels of subsequent sedentary behaviour in participants with low cardiorespiratory fitness: a cross‐sectional study
Authors: Skovgaard Esben Lykke , Obling Kirstine , Maindal Helle Terkildsen , Rasmussen Cuno , Overgaard Kristian 
Published: February 2019

AbstractPerforming physical activity is considered health promoting but may induce a need for subsequent rest periods. This study aimed to determine the within‐day interactions between vigorous physical activity (VPA) and sedentary behaviour (SB) in participants with low cardiorespiratory fitness. We tested the hypothesis that VPA is associated with a temporary subsequent increase in SB. One week of accelerometer data containing a minimum of one 10‐min bout of VPA from 62 participants with low cardiorespiratory fitness (31–50 years old) were obtained from the MILE study. A comparison of SB was made between days with a bout of VPA and days without (control). Due to a positive association between VPA and number and duration of sedentary bouts, the time accumulated in both uninterrupted and total sedentary bouts were 27 (95% CI, 10–45) min and 29 (95% CI, 9–50) min higher on VPA days compared to control days (P < 0.05). Our results indicate that in participants with low cardiovascular fitness, unprompted VPA is positively associated with an increase in subsequent sedentary time. We propose that such VPA‐associated sedentary time may be viewed as part of a healthy activity pattern.
Extended Gravity
Authors: Morales Eduardo , Sheu Gloria , Zahler Andrés 
Published: February 2019

AbstractExporting firms often enter foreign markets that are similar to their previous export destinations. We develop a dynamic model in which a firm’s exports in a market may depend on how similar the market is to the firm’s home country (gravity) and to its previous export destinations (extended gravity). Given the large number of export paths from which forward-looking firms may choose, we use a moment inequality approach to estimate our model. Our estimates indicate that sharing similarities with a prior export destination in terms of geographic location, language, and income per capita jointly reduces the cost of foreign market entry by 69–90%. Reductions due to geographic location (25–38%) and language (29–36%) have the largest effect. Extended gravity thus has a large impact on export entry costs.
Lysobacter psychrotolerans sp. nov., isolated from soil in the Tianshan Mountains, Xinjiang, China
Authors: Luo Yang , Dong Hongqiang , Zhou Meng , Huang Yaolong , Zhang Hua , He Wenliang , Sheng Hongmei , An Lizhe 
Published: February 2019

A novel aerobic bacterial strain, designated ZS60T, with long, rod-shaped, Gram-staining-negative, aerobic cells was isolated from the soil in the Tianshan Mountains, Xinjiang, China. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain ZS60T was affiliated with the genus

Lysobacter

, and was most closely related to

Lysobacter daejeonensis

GH1-9T (96.9 %),

Lysobacter caeni

BUT-8T (96.8 %) and

Lysobacter ruishenii

CTN-1T (96.7 %). The average nucleotide identity values between strain ZS60T,

L. daejeonensis

GH1-9T and

L. ruishenii

CTN-1T were 78.14 and 78.39 %, respectively. The DNA–DNA relatedness between strain ZS60T,

L. daejeonensis

GH1-9T and

L. caeni

BUT-8T were 44.8 and 39.1 %, respectively. The genomic DNA G+C content of the strain ZS60T was 67.7 mol% (draft genome sequence), and Q-8 was the predominant ubiquinone. The major cellular fatty acids of strain ZS60T were iso-C15 : 0 (23.4 %), iso-C17 : 0 (17.2 %) and iso-C17 : 1
ω9c (12.6 %). On the basis of genotypic, phenotypic and biochemical data, strain ZS60T is considered to represent a novel species of the genus

Lysobacter

, for which the name

Lysobacter
psychrotolerans sp. nov. is proposed. The type strain is ZS60T (=CGMCC 1.15509T=NBRC 112614T).
Conditional activation of immune-related signatures and prognostic significance: a pan-cancer analysis
Authors: Roelands Jessica , Hendrickx Wouter , Mall Raghvendra , Saad Mohamad , Halliwill Kyle , Zoppoli Gabriele , Curigliano Giuseppe , Rinchai Darawan , Decock Julie , Delogu Lucia G , Chouchane Lotfi , Wang Ena , Kuppen Peter , Finetti Pascal , Bertucci Francois , Miller Lance D , Galon Jerome , Marincola Francesco M , Ceccarelli Michele , Bedognetti Davide 
Published: February 2019

AbstractBackgroundIt is becoming clear that tumor immune T cell infiltration and its functional orientation have substantial effect on cancer progression, influencing both response to therapy and prognosis. In this pan-cancer study, the previously described Immunologic Constant of Rejection (ICR) signature is used to define opposing immune phenotypes (i.e., immuneactive and immune-silent) across 31 different histologies. We systematically analyze the interconnections between the genetic programming of neoplasms and their immune orientation across different histologies, and the prognostic impact of such interplay. Moreover, we investigated the predictive value of ICR classification across various public datasets of immune checkpoint inhibition therapy.MethodsRNA-seq data of samples from a total of 9,282 patient tumor samples representing 31 cancer types were obtained from The Cancer Genome Atlas (TCGA). We classified each cancer type based on the expression of the ICR gene signature. Oncogenic pathway gene set enrichment and mutational status were analyzed in relation to ICR phenotypes. To explore whether tumorintrinsic attributes associate with the prognostic value of ICR across cancers, we compared mutational load, oncogenic alterations and expression of oncogenic pathways between cancer types using an integrative bioinformatic pipeline.ResultsOur analyses identified a distinct prognostic connotation of ICR depending on cancer histology. We identified several oncogenic pathways whose enrichment inversely correlated with ICR in multiple tumor types. We found several cancer specific pathways that were differentially enriched between tumors in which ICR had a prognostic impact versus the ones in which ICR did not bear any prognostic connotation such as proliferation and TGF-beta signaling. Importantly, this conditional impact of ICR was also validated in the context of immune checkpoint inhibition treatment.ConclusionsWe identified tumor-intrinsic attributes that correlate with immune phenotypes and potentially influence their development. In addition, a relationship was observed between the enrichment of oncogenic pathways and the prognostic significance of the ICR and its predictive value for patients treated with anti-CTLA4 immune checkpoint inhibition. Such information can be used to prioritize potential candidates for therapies aimed at converting immune-silent into immuneactive tumors and to refine stratification algorithms.
The making of an olfactory specialist
Authors: Auer Thomas O. , Khallaf Mohammed A. , Silbering Ana F. , Zappia Giovanna , Ellis Kaitlyn , Hansson Bill S. , Jefferis Gregory S.X.E. , Caron Sophie , Knaden Markus , Benton Richard 
Published: February 2019

AbstractThe evolution of animal behaviour is poorly understood. Despite numerous correlations of behavioural and nervous system divergence, demonstration of the genetic basis of interspecific behavioural differences remains rare. Here we develop a novel neurogenetic model,Drosophila sechellia, a close cousin ofD. melanogasterthat displays profound behavioural changes linked to its extreme host fruit specialisation. Through calcium imaging, we identify olfactory pathways detecting host volatiles. Mutational analysis indicates roles for individual receptors in long- and short-range attraction. Cross-species allele transfer demonstrates that differential tuning of one receptor is important for species-specific behaviour. We identify the molecular determinants of this functional change, and characterise their behavioural significance and evolutionary origin. Circuit tracing reveals that receptor adaptations are accompanied by increased sensory pooling onto interneurons and novel central projection patterns. This work links molecular and neuronal changes to behavioural divergence and defines a powerful model for investigating nervous system evolution and speciation.
Robust network inference using response logic
Authors: Gross Torsten , Wongchenko Matthew , Yan Yibing , Blüthgen Nils 
Published: February 2019

AbstractMotivationA major challenge in molecular and cellular biology is to map out the regulatory networks of cells. As regulatory interactions can typically not be directly observed experimentally, various computational methods have been proposed to disentangling direct and indirect effects. Most of these rely on assumptions that are rarely met or cannot be adapted to a given context.ResultsWe present a network inference method that is based on a simple response logic with minimal presumptions. It requires that we can experimentally observe whether or not some of the system’s components respond to perturbations of some other components, and then identifies the directed networks that most accurately account for the observed propagation of the signal. To cope with the intractable number of possible networks, we developed a logic programming approach that can infer networks of hundreds of nodes, while being robust to noisy, heterogeneous or missing data. This allows to directly integrate prior network knowledge and additional constraints such as sparsity. We systematically benchmark our method on KEGG pathways, and show that it outperforms existing approaches in DREAM3 and DREAM4-challenges. Applied to a perturbation data set on PI3K and MAPK pathways in isogenic models of a colon cancer cell line, it generates plausible network hypotheses that explain distinct sensitivities towards EGFR inhibitors by different PI3K mutants.Availability and ImplementationA Python/Answer Set Programming implementation can be accessed at github.com/GrossTor/response-logic.Contactnils.bluethgen@charite.de
The IL-12– and IL-23–Dependent NK-Cell Response is Essential for Protective Immunity Against SecondaryToxoplasma GondiiInfection
Authors: Ivanova Daria L. , Mundhenke Tiffany M. , Gigley Jason P. 
Published: February 2019

AbstractNatural Killer (NK) cells can develop memory-like features and contribute to long-term immunity in mice and humans. NK cells are critical for protection against acuteT. gondiiinfection. However, whether they contribute to long-term immunity in response to this parasite is unknown. We used a vaccine challenge model of parasite infection to address this question and to define the mechanism by which NK cells are activated during secondary parasite infection. We found NK cells were required for control of secondary infection. NK cells increased in number at the infection site, became cytotoxic and produced IFNγ. Adoptive transfer and NK-cell fate mapping revealed thatT. gondii–experienced NK cells were not intrinsically different from naïve NK cells with respect to their long-term persistence and ability to protect. Thus, they did not develop memory-like characteristics. Instead, a cell-extrinsic mechanism may control protective NK-cell responses during secondary infection. To test the involvement of a cell-extrinsic mechanism, we used anti-IL-12p70 and IL-12p35-/-mice and found that the secondary NK-cell response was not fully dependent on IL-12. IL-23 depletion with anti-IL-23p19in vivosignificantly reduced the secondary NK-cell response, suggesting that both IL-12 and IL-23 were involved. Anti-IL-12p40 treatment, which blocks both IL-12 and IL-23, eliminated the protective secondary NK-cell response, supporting this hypothesis. Our results define a previously unknown protective role for NK cells during secondaryT. gondiiinfection that is dependent on IL-12 and IL-23.
White matter changes in the perforant path in patients with amyotrophic lateral sclerosis
Authors: Mollink J. , Hiemstra M. , Miller K.L. , Huszar I.N. , Jenkinson M. , Raaphorst J. , Wiesmann M. , Ansorge O. , Pallebage-Gamarallage M. , van Cappellen van Walsum A.M. 
Published: February 2019

AbstractAmyotrophic lateral sclerosis (ALS) is a progressive and incurable motor neuron disease. Some ALS patients are affected by a level of cognitive or behavioural decline that meets the criteria for frontotemporal dementia (FTD). ALS and FTD share genetic and pathological features; for example, the deposition of phosphorylated 43 kDa TAR DNA-binding protein (pTDP-43) in the brain. Spreading of pTDP-43 pathology in ALS towards brain areas that connect via the Papez circuit is a possible indicator of progression towards FTD. For example, pTDP-43 aggregates in the granule cells of the hippocampus correlate well with clinically manifest FTD. Here, we test the hypothesis that white matter degeneration of the perforant path – as part of the Papez circuit – in the hippocampus is a feature of ALS, even in the absence of fully developed FTD or deposition of pTDP-43 inclusions in hippocampal granule cells. We used diffusion MRI (dMRI), polarized light imaging (PLI) and immunohistochemical analysis of hippocampus sections from controls (n=5) and ALS patients (n=14) to perform an in-depth study of white matter in the perforant path.The dMRI results show a significant decrease in fractional anisotropy (p=0.01) and an increase in mean diffusivity (p=0.01), axial diffusivity (p=0.03) and radial diffusivity (p=0.03) in the perforant path in ALS patients compared to controls, possibly indicating a loss of white matter fibres. Myelin density (measured with PLI retardance) was lower in ALS patients compared to controls (p=0.05) and correlated with dMRI fractional anisotropy (r=0.52, p=0.03). The dMRI and PLI results were confirmed by the immunohistochemistry; both myelin (proteolipid protein, p=0.03) and neurofilaments (SMI-312, p=0.02) were lower in ALS patients. The activated microglial (CD68) density was similar in ALS and controls. Only two out of the fourteen ALS cases showed pTDP-43 pathology in the dentate gyrus; however, while these two ALS-FTD cases showed reduced myelination in the perforant path, the values were comparable to other ALS cases.We conclude that degeneration of the perforant path occurs in ALS patients and that this may occur before, or independent of, pTDP-43 aggregation in the dentate gyrus of the hippocampus. Future research should focus on correlating the degree of clinically observed cognitive decline to the amount of white matter atrophy in the perforant path.
Silicone Oil-Induced Ocular Hypertension in Mouse Models Glaucomatous Neurodegeneration and Neuroprotection
Authors: Zhang Jie , Li Liang , Huang Haoliang , Webber Hannah C. , Zhuang Pei , Liu Liang , Dalal Roopa , Tang Peter H. , Mahajan Vinit B. , Sun Yang , Li Shaohua , Zhang Mingchang , Goldberg Jeffrey Louis , Hu Yang 
Published: February 2019

AbstractUnderstanding the molecular mechanism of glaucoma and development of neuroprotectants are significantly hindered by the lack of a reliable animal model that accurately recapitulates human glaucoma. Here we sought to develop a mouse model for the secondary glaucoma that is often observed in humans after silicone oil (SO) blocks the pupil or migrates into the anterior chamber following vitreoretinal surgery. We observed similar intraocular pressure (IOP) elevation after intracameral injection into mouse eyes of SO, and removing the SO allows the IOP level to quickly return to normal. This simple, inducible and reversible mouse model showed dynamic changes of visual function that correlate with progressive RGC loss and axon degeneration. We also used a single AAV vector for the first time to co-express miRNA-based shRNA and a neuroprotective transgene and further validated this model as an effective in vivo means to test neuroprotective therapies by targeting neuronal endoplasmic reticulum stress.
Lotus japonicus symbiosis signaling genes and their role in the establishment of root-associated bacterial and fungal communities
Authors: Zgadzaj Rafal , Thiergart Thorsten , Bozsóki Zoltán , Garrido-Oter Ruben , Radutoiu Simona , Schulze-Lefert Paul 
Published: February 2019

AbstractThe wild legume Lotus japonicus engages in mutualistic symbiotic relationships with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing rhizobia. Using plants grown in natural soil and community profiling of bacterial 16S rRNA genes and fungal internal transcribed spacers (ITS), we examined here the role of the Lotus symbiosis genes RAM1, NFR5, SYMRK, and CCaMK in structuring bacterial and fungal root-associated communities. We found host genotype-dependent community shifts in the root and rhizosphere compartments that were mainly confined to bacteria in nfr5 or fungi in ram1 mutants, whilst symRK and ccamk plants displayed major changes across both microbial kingdoms. We observed in all AM mutant roots an almost complete depletion of a large number of Glomeromycota taxa that was accompanied by a concomitant enrichment of Helotiales and Nectriaceae fungi, suggesting compensatory niche replacement within the fungal community. A subset of Glomeromycota whose colonization is strictly dependent on the common symbiosis pathway was retained in ram1 mutants, indicating that RAM1 is dispensable for intraradical colonization by some Glomeromycoyta fungi. However, intraradical colonization by certain Burkholderiaceae taxa is dependent on AM root infection, thereby revealing a microbial interkingdom interaction. Our findings imply a broad role for Lotus symbiosis genes in structuring the root microbiota.
Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dys-regulation of Epithelial-Mesenchymal Transition and subcellular re-localization of Beta-Catenin
Authors: Bowler Emily H , Smith-Vidal Alex , Lester Alex , Bell Joseph , Wang Zhenghe , Bell Chris , Wang Yihua , Divecha Nullin , Skipp Paul , Ewing Rob M. 
Published: February 2019

AbstractBackgroundDNA methyltransferase I is the primary eukaryotic DNA methyltransferase engaged in maintenance of CpG DNA methylation patterns across the genome. Alteration of CpG methylation patterns and levels is a frequent and significant occurrence across many cancers, and targeted inhibition of Dnmt1 has become an approach of choice for select malignancies. There has been significant interest both in the methyltransferase activity as well as methylation-independent functions of Dnmt1. A previously generated hypomorphic allele of Dnmt1 in HCT116 colorectal cancer cells has become an important tool for understanding Dnmt1 function and how CpG methylation patterns are modulated across the genome. Colorectal cancer cells with the Dnmt1 hypomorphic allele carry a homozygous deletion of exons 3 to 5 of Dnmt1, resulting in greatly reduced Dnmt1 protein expression whilst still exhibiting a limited functional activity and methyltransferase ability. Although this cell model of reduced Dnmt1 levels and function have been used to study the downstream effects on the epigenome and transcriptome, the broader effects of the Dnmt1 hypomorph on the proteome and wider cell signalling are largely unknown.ResultsIn this study, we used quantitative proteomic analysis of nuclear-enriched samples of HCT116 Dnmt1 hypomorph cells to identify signalling pathways and processes dysregulated in the hypomorph cells as compared to wild-type HCT116 cells. Unexpectedly, we observed a clear signature of increased expression of Epithelial-to-Mesenchymal (EMT) in Dnmt1 hypomorph cells. We also observed reduced expression and sub-cellular re-localization of Beta-Catenin in Dnmt1 hypomorph cells. Expression of wild-type Dnmt1 in hypomorph cells or knock-down of wild-type Dnmt1 did not recapitulate or rescue the observed protein profiles in Dnmt1 hypomorph cells suggesting that hypomorphic Dnmt1 causes changes not solely attributableConclusionsIn summary we present the first comprehensive proteomic analysis of the widely studied Dnmt1 hypomorph colorectal cancer cells and identify redistribution of Dnmt1 and its interaction partner Beta-Catenin as well as the dysregulation of EMT related processes and signalling pathways related to the development of a cancer stem cell phenotype.
Feasibility of using a fully immersive virtual reality system for kinematic data collection
Authors: Spitzley Kate A. , Karduna Andrew R. 
Published: February 2019

AbstractCommercially-available Virtual Reality (VR) systems have the potential to be effective tools for simultaneous visual manipulation and kinematic data collection. Previously, these systems have been integrated with research-grade motion capture systems to provide both functionalities; however, they are yet to be used as stand-alone systems for kinematic data collection. This study aimed to validate the HTC VIVE VR system for kinematic data collection by evaluating the accuracy of its position and orientation signals. The VIVE controller and tracker were each compared to a Polhemus Liberty magnetic tracking system sensor for angular and translational measurement error and signal drift. A sensor from each system was mounted to opposite ends of a rigid segment which was driven through fifty rotations and fifty translations. Mean angular errors for both the VIVE tracker and controller were below 0.4°. Mean translational error for both sensors was below 3 mm. Drift in the Liberty signal components was consistently lower than drift in VIVE components. However, all mean rotational drift measures were below 0.1° and all mean translational measures were below 0.35 mm. These data indicate that the HTC VIVE system may be a valid and reliable means of kinematic data collection. However, further investigation is necessary to determine the VIVE’s suitability for capturing extremely minute or high-volume movements.
Direct Visualization of Live Zebrafish Glycan via Single-step Metabolic Labeling with Fluorophore-tagged Nucleotide Sugars
Authors: Hong Senlian , Sahai-Hernandez Pankaj , Traver David , Wu Peng 
Published: February 2019

ABSTRACTDynamic turnover of cell-surface glycans is involved in a myriad of biological events, making this process an attractive target for in vivo molecular imaging. The metabolic glycan labeling coupled with ‘bioorthogonal chemistry’ has paved the way for visulizing glycans in living organisms. However, a two-step labeling sequence is required, which is prone to tissue penetration difficulties of the imaging probes. Here, by exploring the substrate promiscuity of endogenous glycosyltransferases, we developed a single-step fluorescent glycan labeling strategy by using fluorophore-tagged analogs of nucleotide sugars directly. Injecting the fluorophore-tagged sialic acid and fucose into the yolk of zebrafish embryos at the one-cell stage enables a systematic imaging of sialylation and fucosylation in live zebrafish embryos at various developmental stages. From these studies, we obtained insights into the role of sialylated and fucosylated glycans in zebrafish hematopoiesis.