bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poststocking Survival of Conditioned and Pond-Reared Compared to Indoor Pellet-Reared Advanced Fingerling Florida Bass
Authors: Trippel Nicholas A. , Porak Wesley F. , Leone Erin H. 
Published: September 2018

Abstract
Supplemental stocking of hatchery Largemouth Bass Micropterus salmoides and Florida Largemouth Bass Micropterus salmoides floridanus (hereafter, Florida Bass) is a common practice around the world, but the results commonly do not meet expectations. Predation upon stocked fish and the inefficiency of stocked fish in capturing wild prey are common reasons for low poststocking survival rates of hatchery fish. Standard protocol for rearing Florida Bass in Florida includes growing fish out in indoor raceways with pellet feed until 5 d prior to stocking, when live prey is introduced. We conducted a 3-year study to determine whether extended conditioning in outdoor ponds, exposure to predators prior to stocking, or rearing in ponds rather than indoor raceways could increase the survival of hatchery-reared Florida Bass. One month after stocking, mean survival for standard hatchery-reared fish that received pellets was 36% (SE = 4.3) across all 3 years. Mean survival was 63% (SE = 4.7) for experimental fish conditioned with predators (E-CWP), 41% (SE = 4.8) for fish conditioned without predators (E-CWOP), and 63% (SE = 5.4) for fish raised on live prey in outdoor ponds in the absence of predators (E-PR). While stocked in research ponds, E-CWP and E-PR fish had higher growth rates than standard pellet-reared fish. During laboratory trials to measure predator avoidance rates, which began 24 h after experimental ponds were stocked, standard pellet-reared fish had a mean 48-h survival rate of 84% (SE = 6.6). Mean 48-h survival for the E-CWP, E-CWOP, and E-PR groups was 96% (SE = 1.9), 84% (SE = 7.2), and 95% (SE = 3.1), respectively. Our experiments indicate that being reared outside or conditioning to a natural environment and exposure to predators may increase poststocking survival of hatchery-reared Florida Bass.
Identification by mass spectrometry of glucosaminylphosphatidylglycerol, a phosphatidylglycerol derivative, produced by Pseudomonas aeruginosa
Authors: Abbes Imen , Rihouey Christophe , Hardouin Julie , Jouenne Thierry , De Emmanuelle , Alexandre Stéphane 
Published: September 2018

RationalePseudomonas aeruginosa is an opportunistic pathogen bacterium widely considered to be an excellent research model in several areas of molecular studies, namely genomics and proteomics. However, its lipid metabolism is still not totally decrypted. While it is known that this bacterium has the particularity to produce phosphatidylcholine, a lipid mainly found in eukaryotes, other singularities are still to be discovered.MethodsP. aeruginosa was grown as planktonic cultures to the stationary state. Membrane pellets were collected and lipids were extracted using the Bligh and Dyer protocol. Lipid extracts were analyzed by Electrospray Ionization Mass Spectrometry (ESI‐MS) using high‐resolution mass spectrometer (LTQ Orbitrap Elite, Thermo Scientific) in the negative mode. MSn spectra were recorded both in the Orbitrap and in the ion trap analyzer (collision‐induced dissociation (CID) or higher energy collision‐induced dissociation (HCD) mode).ResultsWe observed by mass spectrometry and thin layer chromatography that P. aeruginosa produced an unreferenced lipid in classical growth conditions. MS2 analysis of the unknown ion indicates that it is a phosphatidylglycerol derivative. The exact mass shift corresponds to glucosamine which is largely found in the metabolism of this bacterium. MS3 analysis of secondary ions allowed us to conclude that this lipid is a glucosaminylphosphatidylglycerol, a phosphatidylglycerol derivative containing a glucosamine substituted at C4.ConclusionsWe show here that P. aeruginosa is able to produce glucosaminylphosphatidylglycerols via a probable esterification of phosphatidylglycerols by glucosamine.
Concise Review: TLR Pathway-miRNA Interplay in Mesenchymal Stromal Cells: Regulatory Roles and Therapeutic Directions
Authors: Abdi Jahangir , Rashedi Iran , Keating Armand 
Published: September 2018

AbstractMesenchymal stromal cells (MSCs) deploy Toll-like receptors (TLRs) to respond to exogenous and endogenous signals. Activation of TLR pathways in MSCs alters their inflammatory profile and immunomodulatory effects on cells from both the innate and adaptive immune systems. Micro-RNAs (miRNAs), whose expression is modulated by TLR activation, can regulate inflammatory responses by targeting components of the TLR signaling pathways either in MSCs or in the cells with which they interact. Here, we review how the miRNA-TLR pathway axis can regulate the immunomodulatory functions of MSCs, including their interactions with monocytes/macrophages and natural killer cells, and discuss the therapeutic implications for MSC-based therapies.
LncRNA WTAPP1 Promotes Migration and Angiogenesis of Endothelial Progenitor Cells via MMP1 Through MicroRNA 3120 and Akt/PI3K/Autophagy Pathways
Authors: Li Wen-Dong , Zhou Dong-Ming , Sun Li-Li , Xiao Lun , Liu Zhao , Zhou Min , Wang Wen-Bin , Li Xiao-Qiang 
Published: September 2018

Abstract
Efficient recruitment and angiogenesis of endothelial progenitor cells (EPCs) are critical during a thrombus event. However, the details of EPC recruitment and the regulation of angiogenesis have not been fully determined. The aim of this study was to determine the role of the long noncoding (lnc)RNA Wilms tumor 1 associated protein pseudogene 1 (WTAPP1) in regulation of the migration and angiogenesis of EPCs. EPCs were isolated from human peripheral blood and characterized by flow cytometry, after which lentivirus-mediated lncRNA WTAPP1 overexpression and knockdown were performed. Scratch assay, Transwell assay, and in vitro and in vivo tube formation assays were performed to measure cell migration, invasion, and angiogenic abilities, respectively. Moreover, a microarray screen, bioinformatic prediction, and quantitative PCR and Western blot of miRNAs interacting with lncRNA WTAPP1 were conducted. Western blot was carried out to elucidate the relationship among WTAPP1, miR-3120-5P, and MMP-1 in the autophagy pathway. WTAPP1 positively regulated migration, invasion, and in vitro and in vivo tube formation in EPCs by increasing MMP-1 expression and activating PI3K/Akt/mTOR signaling. Furthermore, WTAPP1 contains a putative miR-3120-5P binding site. Suppression of WTAPP1 by miR-3120-5P decreased the level of MMP-1. In addition, we demonstrated that suppression of the autophagy pathway is involved in the effects of WTAPP1 on EPC migration and angiogenesis. The lncRNA WTAPP1, a molecular decoy for miR-3120-5p, regulates MMP-1 expression via the PI3K/Akt and autophagy pathways, thereby mediating cell migration and angiogenesis in EPCs. Acting as a potential therapeutic target, the lncRNA WTAPP1 may play an important role in the pathogenesis of DVT.
The Feelings About genomiC Testing Results (FACToR) Questionnaire: Development and Preliminary Validation
Authors: Li Meng , Bennette Caroline S. , Amendola Laura M. , Ragan Hart M. , Heagerty Patrick , Comstock Bryan , Tarczy‐Hornoch Peter , Fullerton Stephanie M. , Regier Dean A. , Burke Wylie , Trinidad Susan B. , Jarvik Gail P. , Veenstra David L. , Patrick Donald L. 
Published: September 2018

AbstractThe purpose of this study was to develop a brief instrument, the Feelings About genomiC Testing Results (FACToR), to measure the psychosocial impact of returning genomic findings to patients in research and clinical practice. To create the FACToR, we modified and augmented the Multidimensional Impact of Cancer Risk Assessment (MICRA) questionnaire based on findings from a literature review, two focus groups (N = 12), and cognitive interviews (N = 6). We evaluated data from 122 participants referred for evaluation for inherited colorectal cancer or polyposis from the New EXome Technology in (NEXT) Medicine Study, an RCT of exome sequencing versus usual care. We assessed floor and ceiling effects of each item, conducted principal component analysis to identify subscales, and evaluated each subscale’s internal consistency, test‐retest reliability, and construct validity. After excluding items that were ambiguous or demonstrated floor or ceiling effects, 12 items forming four distinct subscales were retained for further analysis: negative emotions, positive feelings, uncertainty, and privacy concerns. All four showed good internal consistency (0.66–0.78) and test‐retest reliability (0.65–0.91). The positive feelings and the uncertainty subscales demonstrated known‐group validity. The 12‐item FACToR with four subscales shows promising psychometric properties on preliminary evaluation in a limited sample and needs to be evaluated in other populations.
Transition From Low‐K to High‐K Calc‐Alkaline Magmatism at Approximately 84 Ma in the Eastern Pontides (NE Turkey): Magmatic Response to Slab Rollback of the Black Sea
Authors: Liu Ze , Zhu Di‐Cheng , Wang Qing , Eyuboglu Yener , Zhao Zhi‐Dan , Liu Sheng‐Ao , Xu Li‐Juan 
Published: September 2018

AbstractCompositional changes of magma in space and time can be used to infer mantle dynamics and crust‐mantle interaction that are responsible for the generation of magma and evolution. This study reveals, for the first time, the presence of magma compositional transition at approximately 84 Ma in the eastern Pontides arc (NE Turkey), providing important insights into the mantle dynamics responsible for the generation of the extensive Late Cretaceous arc magmatism. The Late Cretaceous granitoids can be divided geochemically into two groups. Group I samples were emplaced at 91–86 Ma and are characterized by low K2O/Na2O, whereas Group II samples were emplaced at 83–78 Ma and display high K2O/Na2O. Group I samples have positive zirconεHf(t), whole‐rockɛNd(t), and mantle‐like zircon δ18O, which significantly differs from the Group II samples with negative to positiveεHf(t), negative whole‐rock ɛNd(t), and enhanced zircon δ18O. The Nd‐Hf‐O isotopic compositions of the Group I and II samples can be quantitatively interpreted as being derived from partial melting of the low‐K amphibolite source within the juvenile lower arc crust that incorporated 5–30% and 50–60% enriched components from the basement rocks into the magmatic systems, respectively. Considering the occurrences of regional thermal subsidence and extensional structure during the Late Cretaceous, the compositional transition from Group I to II and the coeval magmatic flare‐up represented by Group II samples can be linked with the slab rollback of the southward subducting Black Sea (Paleotethys) oceanic lithosphere.
Eruption of a multi-flux-rope system in solar active region 12673 leading to the two largest flares in Solar Cycle 24
Authors: Hou Y. J. , Zhang J. , Li T. , Yang S. H. , Li X. H. 
Published: September 2018

Context. Solar active region (AR) 12673 in 2017 September produced the two largest flares in Solar Cycle 24: the X9.3 flare on September 6 and the X8.2 flare on September 10.
Aims. We attempt to investigate the evolutions of the two large flares and their associated complex magnetic system in detail.
Methods. Combining observations from the Solar Dynamics Observatory and results of nonlinear force-free field (NLFFF) modeling, we identify various magnetic structures in the AR core region and examine the evolution of these structures during the flares.
Results. Aided by the NLFFF modeling, we identify a double-decker flux rope configuration above the polarity inversion line (PIL) in the AR core region. The north ends of these two flux ropes were rooted in a negative- polarity magnetic patch, which began to move along the PIL and rotate anticlockwise before the X9.3 flare on September 6. The strong shearing motion and rotation contributed to the destabilization of the two magnetic flux ropes, of which the upper one subsequently erupted upward due to the kink-instability. Then another two sets of twisted loop bundles beside these ropes were disturbed and successively erupted within five minutes like a chain reaction. Similarly, multiple ejecta components were detected as consecutively erupting during the X8.2 flare occurring in the same AR on September 10. We examine the evolution of the AR magnetic fields from September 3 to 6 and find that five dipoles emerged successively at the east of the main sunspot. The interactions between these dipoles took place continuously, accompanied by magnetic flux cancellations and strong shearing motions.
Conclusions. In AR 12673, significant flux emergence and successive interactions between the different emerging dipoles resulted in a complex magnetic system, accompanied by the formations of multiple flux ropes and twisted loop bundles. We propose that the eruptions of a multi-flux-rope system resulted in the two largest flares in Solar Cycle 24.
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Authors: Piližota Ivana , Train Clément-Marie , Altenhoff Adrian , Redestig Henning , Dessimoz Christophe 
Published: September 2018

Abstract

Motivation
As the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably and often remains poor, affecting downstream analyses. This is particularly true when fragments of the same gene are annotated as distinct genes, which may cause them to be mistaken as paralogs.

Results
In this study, we introduce two novel phylogenetic tests to infer non-overlapping or partially overlapping genes that are in fact parts of the same gene. One approach collapses branches with low bootstrap support and the other computes a likelihood ratio test. We extensively validated these methods by (i) introducing and recovering fragmentation on the bread wheat, Triticum aestivum cv. Chinese Spring, chromosome 3B; (ii) by applying the methods to the low-quality 3B assembly and validating predictions against the high-quality 3B assembly; and (iii) by comparing the performance of the proposed methods to the performance of existing methods, namely Ensembl Compara and ESPRIT. Application of this combination to a draft shotgun assembly of the entire bread wheat genome revealed 1221 pairs of genes that are highly likely to be fragments of the same gene. Our approach demonstrates the power of fine-grained evolutionary inferences across multiple species to improving genome assemblies and annotations.

Availability and implementation
An open source software tool is available at https://github.com/DessimozLab/esprit2.

Supplementary information
Supplementary data are available at Bioinformatics online.
SCOP: a novel scaffolding algorithm based on contig classification and optimization
Authors: Li Min , Tang Li , Wu Fang-Xiang , Pan Yi , Wang Jianxin 
Published: September 2018

AbstractMotivationScaffolding is an essential step during the de novo sequence assembly process to infer the direction and order relationships between the contigs and make the sequence assembly results more continuous and complete. However, scaffolding still faces the challenges of repetitive regions in genome, sequencing errors and uneven sequencing depth. Moreover, the accuracy of scaffolding greatly depends on the quality of contigs. Generally, the existing scaffolding methods construct a scaffold graph, and then optimize the graph by deleting spurious edges. Nevertheless, due to the wrong joints between contigs, some correct edges connecting contigs may be deleted.ResultsIn this study, we present a novel scaffolding method SCOP, which is the first method to classify the contigs and utilize the vertices and edges to optimize the scaffold graph. Specially, SCOP employs alignment features and GC-content of paired reads to evaluate the quality of contigs (vertices), and divide the contigs into three types (True, Uncertain and Misassembled), and then optimizes the scaffold graph based on the classification of contigs together with the alignment of edges. The experiment results on the datasets of GAGE-A and GAGE-B demonstrate that SCOP performs better than 12 other competing scaffolders.Availability and implementationSCOP is publicly available for download at https://github.com/bioinfomaticsCSU/SCOP.Supplementary informationSupplementary data are available at Bioinformatics online.
Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes
Authors: Patterson Nathan Heath , Yang Ethan , Kranjec Elizabeth-Ann , Chaurand Pierre 
Published: September 2018

Abstract

Motivation
MALDI imaging mass spectrometry (IMS) has been successfully used to image a variety of biomolecules. Imaging of the many classes of biomolecules is often achieved through several incompatible sample preparations. Thus, multiple datasets must be acquired from multiple tissue sections to obtain a total molecular overview of a single sample. Addressing the need for single datasets from multiple IMS analyses, we developed the R package RegCombIMS as an extension of R package Cardinal to co-register, combine and create single IMS datasets acquired from serial sections of tissue.

Results
Dataset recombination and analysis is achieved by registration of the IMS datasets to a single coordinate space. The workflow allows for correlation of ions from IMS acquisitions that require incompatible sample preparations as well as multivariate analysis to mine the combined dataset for rapid and more thorough molecular query.

Availability and implementation
The source code and example data are freely available at https://github.com/NHPatterson/RegCombIMS. All code was implemented in R.

Supplementary information
Supplementary data are available at Bioinformatics online.
Dissociable Roles Within the Social Brain for Self–Other Processing: A HD-tDCS Study
Authors: Martin A K , Huang J , Hunold A , Meinzer M 
Published: September 2018

Abstract
Theories of right temporoparietal junction (rTPJ) function in social cognition include self–other distinction, self-inhibition, or embodied rotation, whereas the dorsomedial prefrontal cortex (dmPFC) is associated with integrating social information. However, no study has provided causal evidence for dissociable roles of the rTPJ and dmPFC in social cognition. A total of 52 healthy young adults were stratified to receive either dmPFC or rTPJ anodal high-definition transcranial direct current stimulation (HD-tDCS) in a sham-controlled, double-blinded, repeated measures design. Self–other processing was assessed across implicit and explicit level 1 (line-of-sight) and level 2 (mental rotation) visual perspective taking (VPT) tasks, and self–other effects on memory. DmPFC stimulation selectively increased the influence of the allocentric perspective during egocentric perspective taking, indexed by an increase in congruency effect across explicit VPT tasks. Moreover, dmPFC stimulation removed the self-reference effect in episodic memory by increasing the recognition of other and decreasing the recognition of self-encoded words. Stimulation of the rTPJ resulted in improved inhibition of the egocentric-perspective during level 2 VPT only, indexed by a reduction of the congruency effect when taking the allocentric perspective. This research supports theories suggesting that the rTPJ facilitates embodied mental rotation of the self into an alternate perspective, whereas the dmPFC integrates social information relevant to self-directed processes.
Age-Related Decline in Learning Deterministic Judgment-Based Sequences
Authors: Dang Layla , Larson Sylvia P , Gluck Mark A , Petok Jessica R 
Published: September 2018

AbstractObjectivesBecause sequence learning is integral to cognitive functions across the life span, the present study examined the effect of healthy aging on deterministic judgment-based sequence learning.MethodsCollege-aged, younger–old (YO), and older–old (OO) adults completed a judgment-based sequence learning task which required them to learn a full sequence by chaining together single stimulus–response associations in a step-by-step fashion.ResultsResults showed that younger adults outperformed YO and OO adults; older adults were less able to acquire the full sequence and committed significantly more errors during learning. Additionally, higher sequence learning errors were associated with advancing age among older adults, even when controlling for other factors known to contribute to sequence learning abilities. Such impairments were selective to learning sequential information, because adults of all ages performed equivalently on postlearning probe trials, as well as on learning simple stimulus–response associations.DiscussionThis pattern of age deficits during deterministic sequence learning challenges past reports of age preservation. Though the neural processes underlying learning cannot be determined here, our patterns of age deficits and preservation may reflect different brain regions that are involved in the task phases, adding behavioral evidence to the emerging hypothesis of frontostriatal declines despite spared hippocampal function with age.
The next level of play
Authors: Gauvin Jean-François 
Published: September 2018

Abstract
Although teaching science is considered a serious business, toys and sometimes entertaining spectacles have been at the very heart of such an endeavour over the past 300 years. Using, among other things, the Collection of Historical Scientific Instruments as a material historical source, this article describes how the ‘magical’ effects of a Cartesian Devil or a solar microscope, the deafening explosion of a volcano, the building (and breaking) of a measuring apparatus, and the playing with mathematical and quantum toys diligently imparted vast areas of scientific knowledge to Harvard University students between 1730 and 1970. Playing with science – and with scientific instruments – is examined here as a valued pedagogical strategy deployed by generations of teachers, who saw in the material culture of science a renewable resource for training the mind and acquiring manual skills. It also allows us to study an important collection of objects from an unusual perspective.
Shrinkage improves estimation of microbial associations under different normalization methods
Authors: Badri Michelle , Kurtz Zachary D. , Bonneau Richard , Müller Christian L. 
Published: September 2018

ABSTRACTConsistent estimation of associations in microbial genomic survey count data is fundamental to microbiome research. Technical limitations, including compositionality, low sample sizes, and technical variability, obstruct standard application of association measures and require data normalization prior to estimating associations. Here, we investigate the interplay between data normalization and microbial association estimation by a comprehensive analysis of statistical consistency. Leveraging the large sample size of the American Gut Project (AGP), we assess the consistency of the two prominent linear association estimators, correlation and proportionality, under different sample scenarios and data normalization schemes, including RNA-seq analysis work flows and log-ratio transformations. We show that shrinkage estimation, a standard technique in high-dimensional statistics, can universally improve the quality of association estimates for microbiome data. We find that large-scale association patterns in the AGP data can be grouped into five normalization-dependent classes. Using microbial association network construction and clustering as examples of exploratory data analysis, we show that variance-stabilizing and log-ratio approaches provide for the most consistent estimation of taxonomic and structural coherence. Taken together, the findings from our reproducible analysis workflow have important implications for microbiome studies in multiple stages of analysis, particularly when only small sample sizes are available.