bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae
Authors: Fiore Cara L. , Alexander Harriet , Kido Soule Melissa C. , Kujawinski Elizabeth B. 
Published: December 2018

AbstractPhosphorus (P) limits primary production in regions of the surface ocean, and many plankton species exhibit specific physiological responses to P-deficiency. The metabolic response of Micromonas pusilla, an ecologically relevant marine photoautotroph, to P-deficiency was investigated using environmental metabolomics and comparative genomics. The concentrations of some intracellular metabolites were elevated in the P-deficient cells (e.g., xanthine, inosine) and genes involved in the associated metabolic pathways shared a predicted conserved amino acid motif in the non-coding regions of each gene. The presence of the conserved motif suggests that these genes may be co-regulated, and the motif may constitute a regulatory element for binding a transcription factor, specifically that of Psr1 (Phosphate starvation response,), first described in the alga, Chlamydomonas reinhardtii. A putative phosphate starvation response gene (psr1-like) was identified in M. pusilla with homology to well characterized psr1/phr1 genes in algae and plants, respectively. This gene appears to be present and expressed in other marine algal taxa (e.g., Emiliania huxleyi) in field sites that are chronically phosphorus-limited. Results from the present study have implications for understanding phytoplankton taxon-specific roles in mediating P cycling in the ocean.
PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution
Authors: Gordon Sean P. , Levy Joshua J. , Vogel John P. 
Published: December 2018

AbstractExisting methods for assigning sequences to individual species from pooled DNA samples rely on differences in genome properties like GC content or sequences from related species. These approaches do not work for closely related species where gross features are indistinguishable and related genomes are lacking. We describe a method and associated software package that uses rapidly evolving repetitive DNA to circumvent these limitations. By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes without any prior knowledge. This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.
OCHROdb: a comprehensive, quality checked database of open chromatin regions from sequencing data
Authors: Shooshtari Parisa , Feng Samantha , Nelakuditi Viswateja , Foong Justin , Brudno Michael , Cotsapas Chris 
Published: December 2018

ABSTRACTInternational consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.
Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to modulate chromatin structure and gene expression
Authors: Miyaji Mary , Furuta Ryohei , Hosoya Osamu , Sano Kuniaki , Hara Norikazu , Kuwano Ryozo , Kang Jiyoung , Tateno Masaru , Tsutsui Kimiko M. , Tsutsui Ken 
Published: December 2018

AbstractBackgroundType II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T-segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be placed far from each other on the same chromosome. However, no direct evidence for this to occur has been described so far due to lack of proper methodology.ResultsThe beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. To elucidate the enzyme’s role in the process, here we devise a genome-wide mapping technique for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It became clear that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that the DSP sites are intertwined or knotted and topo IIβ is engaged in unknotting reaction that leads to chromatin decondensation and gene regulation.ConclusionsWhen combined with categorized gene expression analysis, the model-based prediction of DSP sites reveals that DSP is one of the key factors for topo IIβ-dependency of neuronal gene regulation.
Experimental evolution of independent genetic pathways for resistance toPseudomonas aeruginosapathogenicity within the nematodeCaenorhabditis remanei
Authors: Archer Heather , Phillips Patrick C. 
Published: December 2018

ABSTRACTPathogenic host-microbe interactions can result from continuous evolution of a host’s ability to resist infection and a pathogen’s ability to survive and replicate.Pseudomonas aeruginosais a versatile and opportunistic pathogen, ubiquitous in the environment, and capable of damaging plants, vertebrates, and invertebrates. Previous studies in nematodes suggest that the pathogenic effects ofP. aeruginosacan result from multiple distinct pathways: a toxin-based effect that kills within a few hours and a generalized virulence that kills over the course of multiple days. Using experimental evolution in the highly polymorphic nematodeCaenorhabditis remanei, we show that nematode resistance to the two modes of pathogenesis inP. aeruginosaevolves through genetically independent pathways. These results demonstrate that multiple virulence patterns in a pathogen can result in multiple responses in the host, and the genetic lines established here create resources for further exploration of the genetic basis for resistance toP. aeruginosa.
Implementation of the Perfect Plasticity Approximation with biogeochemical compartments in R
Authors: Erickson Adam , Strigul Nikolay 
Published: December 2018

AbstractModeling forest ecosystems is a landmark challenge in science, due to the complexity of the processes involved and their importance in predicting future planetary conditions. While there are a number of open-source forest biogeochemistry models, few papers exist detailing the software development approach used to develop these models. This has left many forest biogeochemistry models large, opaque, and/or difficult to use, typically implemented in compiled languages for speed. Here, we present a forest biogeochemistry model from the SORTIE-PPA class of models, PPA-SiBGC. Our model is based on the Perfect Plasticity Approximation with simple biogeochemistry compartments and uses empirical vegetation dynamics rather than detailed prognostic processes to drive the estimation of carbon and nitrogen fluxes. This allows our model to be used with traditional forest inventory data, making it widely applicable and simple to parameterize. We detail the conceptual design of the model as well as the software implementation in the R language for statistical computing. Our aim is to provide a useful tool for the biogeochemistry modeling community that demonstrates the importance of vegetation dynamics in biogeochemical models.
Single-cell Transcriptomics reveals multi-step adaptations to endocrine therapy
Authors: Hong Sung Pil , Chan Thalia E. , Lombardo Ylenia , Corleone Giacomo , Rotmensz Nicole , Pruneri Giancarlo , McEwen Kirsten R. , Coombes R. Charles , Barozzi Iros , Magnani Luca 
Published: December 2018

AbstractResistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. Partially, this is due to our limited understanding on the effect of ET at the single cell level. In the present study, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare sub-population of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. PA cells show reduced oestrogen receptor α activity but increased features of quiescence and migration. We find evidence for sub-clonal expression of this PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.
SMCR8 negatively regulates AKT and MTORC1 signaling to modulate lysosome biogenesis and tissue homeostasis
Authors: Lan Yungang , Sullivan Peter M. , Hu Fenghua 
Published: December 2018

AbstractThe intronic hexanucleotide expansion in the C9orf72 gene is one of the leading causes of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS), 2 devastating neurodegenerative diseases. C9orf72 forms a heterodimer with SMCR8 (Smith-Magenis syndrome chromosome region, candidate 8) protein. However, the physiological function of SMCR8 remains to be characterized. Here we report that ablation of SMCR8 in mice results in splenomegaly with autoimmune phenotypes similar to that of C9orf72 deficiency. Furthermore, SMCR8 loss leads to a drastic decrease of C9orf72 protein levels. Many proteins involved in the macroautophagy-lysosome pathways are downregulated upon SMCR8 loss due to elevated activation of MTORC1 and AKT, which also leads to increased spine density in the Smcr8 knockout neurons. In summary, our studies demonstrate a key role of SMCR8 in regulating MTORC1 and AKT signaling and tissue homeostasis.
Isolation of adipose tissue derived regenerative cells from human subcutaneous tissue with or without the use of an enzymatic reagent
Authors: Winnier Glenn E. , Valenzuela Nick , Alt Christopher , Peters-Hall Jennifer , Kellner Joshua , Alt Eckhard U. 
Published: December 2018

ABSTRACTBackgroundFreshly isolated, uncultured autologous adipose derived regenerative cells (ADRCs) have emerged as a promising tool for regenerative cell therapy. The Transpose RT system (InGeneron, Inc., Houston, TX, USA) is a system for isolating ADRCs from adipose tissue, commercially available in Europe as a CE-marked medical device and under clinical evaluation in the United States. This system makes use of the proprietary, enzymatic Matrase Reagent for isolating cells. The present study addressed the question whether the use of Matrase Reagent influences cell yield, cell viability, live cell yield, biological characteristics, physiological functions or structural properties of the ADRCs in final cell suspension.MethodsIdentical samples of subcutaneous adipose tissue from 12 subjects undergoing elective lipoplasty were processed either with or without the use of Matrase Reagent. Then, characteristics of the ADRCs in the respective final cell suspensions were evaluated.ResultsCompared to non-enzymatic isolation, enzymatic isolation resulted in approximately twelve times higher mean cell yield (i.e., numbers of viable cells/ml lipoaspirate) and approximately 16 times more colony forming units. Despite these differences, cells isolated from lipoaspirate both with and without the use of Matrase Reagent were independently able to differentiate into cells of all three germ layers.DiscussionThe data of this study indicate that biological characteristics, physiological functions or structural properties relevant for the intended use were not altered or induced using Matrase Reagent. A comprehensive literature review demonstrated that isolation of ADRCs from lipoaspirate using the Transpose RT system and the Matrase Reagent results in the highest viable cell yield among all published data regarding isolation of ADRCs from lipoaspirate.
The application of trigonometric grey prediction model to average per capita natural gas consumption of households in China
Authors: Wang Qiuping , Liu Subing , Yan Haixia 
Published: December 2018

Purpose
Due to high efficiency and low carbon of natural gas, the consumption of natural gas is increasing rapidly, and the prediction of natural gas consumption has become the focus. The purpose of this paper is to employ a prediction technique by combining grey prediction model and trigonometric residual modification for predicting average per capita natural gas consumption of households in China.

Design/methodology/approach
The GM(1,1) model is utilised to obtain the tendency term, then the generalised trigonometric model is used to catch the periodic phenomenon from the residual data of GM(1,1) model for improving predicting accuracy.

Findings
The case verified the view of Xie and Liu: “When the value of a is less, DGM model and GM(1,1) model can substitute each other.” The combination of the GM(1,1) and the trigonometric residual modification technique can observably improve the predicting accuracy of average per capita natural gas consumption of households in China. The mean absolute percentage errors of GM(1,1) model, DGM(1,1), unbiased grey forecasting model, and TGM model in ex post testing stage (from 2013 to 2015) are 32.5510, 33.5985, 36.9980, and 5.2996 per cent, respectively. The TGM model is suitable for the prediction of average per capita natural gas consumption of households in China.

Practical implications
According to the historical data of average per capita natural gas consumption of households in China, the authors construct GM(1,1) model, DGM(1,1) model, unbiased grey forecasting model, and GM(1,1) model with trigonometric residual modification. The accuracy of TGM is the best. TGM helps to improve the accuracy of GM(1,1).

Originality/value
This paper gives a successful practical application of grey model GM(1,1) with the trigonometric residual modification, where the cyclic variations exist in the residual series. The case demonstrates the effectiveness of trigonometric grey prediction model, which is helpful to understand the modeling mechanism of trigonometric grey prediction model.
Real-time monocular 3D perception with ORB-Features
Authors: Ji Babing , Cao Qixin 
Published: December 2018

Purpose
This paper aims to propose a new solution for real-time 3D perception with monocular camera. Most of the industrial robots’ solutions use active sensors to acquire 3D structure information, which limit their applications to indoor scenarios. By only using monocular camera, some state of art method provides up-to-scale 3D structure information, but scale information of corresponding objects is uncertain.

Design/methodology/approach
First, high-accuracy and scale-informed camera pose and sparse 3D map are provided by leveraging ORB-SLAM and marker. Second, for each frame captured by a camera, a specially designed depth estimation pipeline is used to compute corresponding 3D structure called depth map in real-time. Finally, depth map is integrated into volumetric scene model. A feedback module has been designed for users to visualize intermediate scene surface in real-time.

Findings
The system provides more robust tracking performance and compelling results. The implementation runs near 25 Hz on mainstream laptop based on parallel computation technique.

Originality/value
A new solution for 3D perception is using monocular camera by leveraging ORB-SLAM systems. Results in our system are visually comparable to active sensor systems such as elastic fusion in small scenes. The system is also both efficient and easy to implement, and algorithms and specific configurations involved are introduced in detail.
Identifying and ranking CSFs for KM implementation in urban water and sewage companies using ISM-DEMATEL technique
Authors: Mousavizade Faeze , Shakibazad Mohammad 
Published: December 2018

PurposeThis paper aims to study the critical success factors (CSF) of knowledge management (KM) in Iranian urban water and sewage companies (IUWSC) using interpretive structural modeling (ISM)-decision-making trial and evaluation laboratory (DEMATEL) method.Design/methodology/approachThrough the literature review among many key factors of KM success, nine factors were selected as the main factors. After confirming the related indices by industry experts, a questionnaire was distributed among them for determining the relationship between the relevant components. Using ISM-DEMATEL approach, a structural model was formed and then the causal relationship among factors was visualized through a cause-effect relationship diagram.FindingsThe analysis of the results showed that among the studied factors, strategies and goals would have the greatest impact on success of KM implementation and senior management support, and teamwork and organizational culture are other CSFs of KM in IUWSC. In the end, the author’s proposed model for implementation of KM was presented based on the results for the status quo of the studied community.Practical implicationsThe set of CSFs can act as a guideline for organizations to ensure that basic factors and issues are covered during implementation KM. Moreover, it provides a clue for effective development of KM in a stepwise approach.Originality/valueThis survey is probably the first to provide an integrated view of CSFs for implementation KM in IUWSC. It is hoped to give valuable information to help this business sector to accomplish KM effectively.
Organizational knowledge retention and knowledge loss
Authors: Levallet Nadège , Chan Yolande E. 
Published: December 2018

PurposeThis paper aims to examine the effectiveness of organizational information technology (IT)-based and non-IT-based knowledge transfer mechanisms (KTMs) for the retention of different types of knowledge from mobile experts. It differentiates among four types of knowledge loss (KL), namely, conscious knowledge (i.e. individual explicit knowledge that can be codified); codified knowledge (i.e. explicit knowledge captured at the social level); automatic knowledge (i.e. implicit individual knowledge); and collective knowledge (i.e. implicit knowledge embedded in the organization).Design/methodology/approachA research framework connecting the organizational knowledge retention (KR) cycle to KL is developed and an exploratory analysis is conducted using data from two case studies in the Canadian federal public service. Findings are confirmed using a third government agency.FindingsWithout the right processes in place for organizational knowledge retrieval and reuse, the KR cycle is not complete, leading to KL. The lack of available social KTMs for the conversion of individual to social objectified knowledge leads to KL. KTMs shortcomings increase the risk of automatic and objectified KL.Research limitations/implicationsExploratory results demonstrate that KL does not always equate to lack of KR. Implementing knowledge-specific organizational KTMs is important to encourage the retention of individual knowledge at the social level. Propositions and a framework are developed for future research.Practical implicationsMobile experts hold valuable knowledge at high risk of being lost by organizations. This paper provides managers with a set of guidelines to develop a knowledge-specific strategy focused on KTMs that increase KR and mitigate KL.Originality/valueThis paper challenges the assumption that KL only results from poor retention and studies both retention and loss to identify additional types of unintentional loss that occur when individual knowledge is not converted to social knowledge.
Validity and accuracy of the Whooley questions to identify maternal distress in Dutch pregnant women
Authors: Fontein-Kuipers Yvonne , Jomeen Julie 
Published: December 2018

Purpose
The purpose of this paper is to investigate the validity and accuracy of the Whooley questions for routine screening of maternal distress in Dutch antenatal care.

Design/methodology/approach
In this cohort design, the authors evaluated self-reported responses to the Whooley questions against the Edinburgh Depression Scale screening for antenatal depression, State-Trait Anxiety Inventory for general anxiety and the pregnancy-related anxiety questionnaire-revised screening for pregnancy-related anxiety, among Dutch pregnant women during the first and third trimester of pregnancy. The authors used standard diagnostic performance measures for the two case-finding items.

Findings
The Whooley items in this study showed a higher specificity than sensitivity. The Whooley results showed good evidence to identify women who are depressed or (trait)anxious in both trimesters of pregnancy, but the results showed weak to moderate evidence to identify pregnancy-related anxiety. The Whooley items had a low to moderate predictive ability for depression, trait-anxiety and pregnancy-related anxiety and a good ability for negative case-finding. The Whooley items proved to be more able to report how effective the case-finding questions are in identifying women without depression, trait-anxiety and pregnancy-related anxiety (ruling out) rather than how effective these are in identifying women with depression, trait-anxiety and pregnancy-related anxiety (ruling in). The Whooley items were accurate in identifying depression and trait-anxiety in both trimesters but were not very accurate to identify pregnancy-related anxiety.

Research limitations/implications
Assessment of pregnancy-related anxiety using a case-finding tool requires further attention.

Practical implications
The two-item Whooley case-finding tool has shown good utility as a screening instrument for maternal distress. The continuous assessment of maternal emotional health during the childbearing period or, at least, revisiting the topic, would both support the woman and the midwife in regarding perinatal emotional wellbeing as an important remit of midwifery care.

Originality/value
A novel aspect of this paper is the proposition of applying the Whooley questions at later stages of pregnancy or presenting the Whooley questions in a written or digital form.