bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoplasmic translocation of nuclear lysine-specific demethylase-1 (LSD1/KDM1A) in human hepatoma cells is induced by its inhibitors
Authors: Yabuta Suemi , Shidoji Yoshihiro 
Published: March 2018

ABSTRACTHistone-modifiable lysine-specific demethylase-1 (LSD1/KDM1A) is often upregulated in many cancers, including hepatoma, and is regarded as oncoprotein. We previously reported that the hepatoma-preventive geranylgeranoic acid (GGA) inhibits KDM1A activity at the same IC50as that of the clinically used drug tranylcypromine, a verified inhibitor of KDM1A. Here, we report that these inhibitors induced cytoplasmic translocation of nuclear KDM1A in a human hepatoma-derived cell line. Immunofluorescence studies revealed cytoplasmic localization of KDM1A, 3 h after addition of GGA or tranylcypromine in HuH-7 cells. Geranylgeraniol and all-transretinoic acid were both unable to induce translocation of nuclear KDM1A, whereas farnesoic acid showed the weak activity. Furthermore, GGA did not affect subcellular localization of another histone lysine-specific demethylase, KDM5A. This suggests that the inhibitor-induced translocation of nuclear KDM1A to the cytoplasm is specific for KDM1A. These data demonstrate for the first time that KDM1A inhibitors specifically induce the cytoplasmic translocation of nuclear KDM1A.AbbreviationsATRAall-transretinoic acidCoRESTcorepressor for element 1-silencing transcription factorDICdifferential interference contrastFAfarnesoic acidGGOHgeranylgeraniolGGAgeranylgeranoic acidLSD1/KDM1Alysine-specific demethylase-1pHH3phospho-histone H3(Ser10)TCPtrans-2-phenylcyclopropylamine
segment_liftover: a Python tool to convert segments between genome assemblies
Authors: Gao Bo , Huang Qingyao , Baudis Michael 
Published: March 2018

AbstractThe process of assembling a species’ reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller subsegments if the original segment’s continuity is disrupted in the target assembly. Such a conversion may lead to a relevant degree of data loss in some circumstances such as copy number variation (CNV) analysis, where the quantitative representation of a genomic region takes precedence over base-specific accuracy. segment_liftover aims at continuity-preserving remapping of genome segments between assemblies and provides features such as approximate locus conversion, automated batch processing and comprehensive logging to facilitate processing of datasets containing large numbers of structural genome variation data.
Small differences in learning speed for different food qualities can drive efficient collective foraging in ant colonies
Authors: Oberhauser F. B. , Koch A. , Czaczkes T. J. 
Published: March 2018

AbstractSocial insects frequently make important collective decisions, such as selecting the best food sources. Many collective decisions are achieved via communication, for example by differential recruitment depending on resource quality. However, even species without recruitment can respond to a changing environment on collective level by tracking food source quality.We hypothesised that an apparent collective decision to focus on the highest quality food source can be explained by differential learning of food qualities. Ants may learn the location of higher quality food faster, with most ants finally congregating at the best food source.To test the effect of reward quality and motivation on learning inLasius niger, we trained individual ants to find a reward of various sucrose molarities on one arm of a T-maze in spring and in autumn after one or four days of starvation.As hypothesised, ants learned fastest in spring and lowest in autumn, with reduced starvation leading to slower learning. Surprisingly, the effect of food quality and motivation on the learning speed of individuals which persisted in visiting the feeders was small. However, persistence rates varied dramatically: All ants in spring made all (6) return visits to all food qualities, in contrast to 33% of ants in autumn under low starvation.Fitting the empirical findings into an agent-based model revealed that even a tendency of ants to memorise routes to high quality food sources faster can result in ecologically sensible colony-level behaviour. Low motivation colonies are also choosier, due to increasing sensitivity to food quality.Significance statementCollective decisions of insects are often achieved via communication and/or other interactions between individuals. However, animals can also make collective decisions in the absence of communication.We show that foraging motivation and food quality can affect both route memory and the likelihood to return to the food source and thus mediate selective food exploitation. An agent-based model, implemented with our empirical findings, demonstrates that, at the collective level, even small differences in learning lead to ecologically sensible behaviour: mildly starved colonies are selective for high quality food while highly starved colonies exploit all food sources equally.We therefore suggest that non-interactive factors such as individual learning and the foraging motivation of a colony can mediate or even drive group level behaviour. Instead of accounting collective behaviour exclusively to social interactions, possible contributing individual processes should also be considered.
TRPV1 regulates opioid analgesia during inflammation
Authors: Basso Lilian , Aboushousha Reem , Fan Churmy Yong , Iftinca Mircea , Melo Helvira , Flynn Robyn , Agosti Francina , Hollenberg Morley D. , Thompson Roger , Bourinet Emmanuel , Trang Tuan , Altier Christophe 
Published: March 2018

AbstractAcute inflammation in humans or mice enhances the analgesic properties of opioids. However, the inflammatory transducers that prime opioid receptor signaling in nociceptors are unknown. We found that TRPV1−/− mice are insensitive to peripheral opioid analgesia in an inflammatory pain model. We report that TRPV1 channel activation drives a MAPK signaling pathway accompanied by the shuttling of β-arrestin2 to the nucleus. This shuttling in turn prevents: β-arrestin2-receptor recruitment, subsequent internalization of agonist-bound mu opioid receptor (MOR), and suppression of DAMGO-induced inhibition of N-type calcium current observed upon desensitization. Consequently, inflammation-induced activation of TRPV1 preserves opioid analgesic potency in a mouse model of opioid receptor desensitization. Overall, our work reveals a TRPV1-mediated signaling mechanism, involving β-arrestin2 nuclear translocation, that underlies the peripheral opioid control of inflammatory pain. Our data single out TRPV1 channels as modulators of opioid analgesia.
ARGminer: A web platform for crowdsourcing-based curation of antibiotic resistance genes
Authors: Arango-Argoty G. A. , Guron G. K. P. , Garner E. , Riquelme M.V. , Heath L. S. , Pruden A. , Vikesland P. J. , Zhang L. 
Published: March 2018

ABSTRACTCuration of antibiotic resistance gene (ARG) databases is labor intensive and requires expert knowledge to manually collect, correct, and/or annotate individual genes. Consequently, most existing ARG databases contain only a small number of ARGs (~5k genes) and updates to these databases tend to be infrequent, commonly requiring years for completion and often containing inconsistencies. Thus a new approach is needed to achieve a truly comprehensive ARG database while also maintaining a high level of accuracy. Here we propose a new web-based curation system, ARGminer, that supports the annotation and inspection of several key attributes of potential ARGs, including gene name, antibiotic category, resistance mechanism, evidence for mobility and occurrence in clinically-important bacterial strains. Here we employ crowdsourcing as a novel strategy to overcome limitations of manual curation and expand curation capacity towards achieving a truly comprehensive and perpetually up-to-date database. Further, machine learning is employed as a powerful means to validate database curation, drawing from natural language processing to infer correct and consistent nomenclature for each potential ARG. We develop and validate the crowdsourcing approach by comparing performances of multiple cohorts of curators with varying levels of expertise, demonstrating that ARGminer is a time and cost efficient means of achieving accurate ARG curation. We further demonstrate the reliability of a trust validation filter for rejecting input generated by spammers. Crowdsourcing was found to be as accurate as expert annotation, with an accuracy >90% for the annotation of a diverse test set of ARGs. The ARGminer public search platform and database is available at http://bench.cs.vt.edu/argminer.
Further studies of ion channels in the electroreceptor of the skate through deep sequencing, cloning and cross species comparisons
Authors: Clusin William T. , Wu Ting-Hsuan , Shi Ling-Fang , Kao Peter N. 
Published: March 2018

AbstractOur comparative studies seek to understand the structure and function of ion channels in cartilaginous fish that can detect very low voltage gradients in seawater. The principal channels of the electroreceptor include a calcium activated K channel, whose α subunit is Kcnma1, a voltage-dependent calcium channel, Cacna1d, and a relatively uncharacterized K channel which interacts with the calcium channel to produce fast (20 Hz) oscillations. Large conductance calcium-activated K channels (BK) are comprised of four α subunits, encoded by Kcnma1 and modulatory β subunits of the Kcnmb class. We recently cloned and published the skate Kcnma1 gene and most of Kcnmb4 derived from using purified mRNA of homogenized isolated electroreceptors. Bellono et al. have recently performed RNA sequencing (RNA-seq) on purified mRNA from skate electroreceptors and found several ion channels including Kcnma1. We searched the the Bellono et al RNA-seq repository for additional channels and subunits. Our most significant findings are the presence of two Shaker type voltage dependent potassium channel sequences which are grouped together as isoforms in the data repository. The larger of these is a skate ortholog of the voltage dependent fast potassium channel Kv1.1, which is expressed at appreciable levels and seems likely to explain the 20 Hz oscillations believed to occur in vivo. The second was more similar to Kv1.5 than to Kv1.1 but was somewhat atypical. We also found a beta subunit sequence (Kcnab2) which appears not to cause fast inactivation due to specific structural features. The new channels and subunits were verified by RT-PCR and the Kv1.1 sequence was confirmed by cloning. We also searched the RNA-seq repository for accessory subunits of the calcium activated potassium channel, Kcnma1, and found a computer generated assembly that contained a complete sequence of its beta subunit, Kcnmb2. Skate Kcnmb2 has a total of 279 amino acids, with 51 novel amino acids at the N-terminus which may play a specific physiological role. This sequence was confirmed by PCR and cloning. However, skate Kcnmb2 is expressed at low levels in the electroreceptor compared to Kcnma1 and skate Kcnmb1 (beta1) is absent. The evolutionary origin of the newly described channels and subunits was studied by aligning skate sequences with human sequences and those found in related fish: the whale shark (R. typus) an elasmobranch, and ghost shark (C.milii). There is also homology with the lamprey, which has electroreceptors. An evolutionary tree is presented. Further research should include focusing on the subcellular locations of these channels in the receptor cells, their gating behavior, and the effects of accessory subunits on gating.
Multiplexedin situprotein imaging using DNA-barcoded antibodies with extended hybridization chain reactions
Authors: Wang Yu , Zeng Yitian , Saka Sinem K. , Xie Wenxin , Goldaracena Isabel , Kohman Richie E. , Yin Peng , Church George M. 
Published: March 2018

AbstractImmunofluorescence (IF) imaging using antibodies to visualize specific biomolecules is a widely used technique in both biological and clinical laboratories. Standard IF imaging methods using primary antibodies followed by secondary antibodies have low multiplexing capability due to limited availability of primary antibodies raised in different animal species. Here, we used a DNA-based signal amplification method, Hybridization Chain Reaction (HCR), to replace secondary antibodies to achieve multiplexed imaging using primary antibodies of the same species with superior signal intensity. To enable imaging with DNA-conjugated antibodies, we developed a new antibody staining protocol to minimize nonspecific binding of antibodies caused by conjugated DNA oligonucleotides. We also expanded the HCR hairpin pool from previously published 5 to 13 for highly multiplexedin situimaging. We finally demonstrated multiplexedin situprotein imaging using the technique in both cultured cells and mouse retina sections.
Efficient expression of genes in the Drosophila germline using a UAS-promoter free of interference by Hsp70 piRNAs
Authors: DeLuca Steven Z. , Spradling Allan C. 
Published: March 2018

ABSTRACTControlling the expression of genes using a binary system involving the yeast GAL4 transcription factor has been a mainstay ofDrosophila melanogasterdevelopmental genetics for twenty-five years. However, most existing GAL4 expression constructs only function effectively in somatic cells, but not in germ cells during oogenesis, for unknown reasons. A special UAS promoter, UASp was created that does express during oogenesis, but the need to use different constructs for somatic and female germline cells has remained a significant technical limitation. Here we show that the expression problem of UASt and many other Drosophila molecular tools in germline cells is caused by their coreHsp70promoter sequences, which are targeted in female germ cells byHsp70-directed piRNAs generated from endogenousHsp70gene sequences. In a genetic background lacking genomicHsp70genes and associated piRNAs, UASt-based constructs function effectively during oogenesis. By reducingHsp70sequences targeted by piRNAs, we created UASz, which functions better than UASp in the germline and like UASt in somatic cells.
Industrial proximity and vertical integration of multinational firms
Authors: Yoon Haeyeon , Hur Jung 
Published: March 2018

Purpose
With the rise of foreign direct investment and global value chain, firms organize their plant allocation across countries to take advantage of production cost reduction opportunities and market access. The purpose of this paper is to investigate the production-supply strategies of Korean firms over foreign and domestic affiliates, using industrial proximity between Korean parent firms and their affiliates.

Design/methodology/approach
In this paper first, using the Survey of Business Activities provided by Statistics Korea, the authors build a matching data set between a parent firm and each affiliate both in domestic and foreign countries. Second, the authors define their vertical relationship based on the input requirement coefficients of the Input-Output table (IO table). Furthermore, using the same IO table, the authors define the proximity for the pairs of the parent firm and the affiliates in domestic and foreign markets. Then, the authors test the relationship between the parent firm’s choice for foreign affiliate and their proximity index.

Findings
The main result shows that the stronger the industrial proximity between a final good producing firm and its input supplying affiliate is, the more likely the cross-border vertical integration is to be observed than the domestic vertical integration. Also, the authors find that the firms whose production structure accords the main result outperform and conduct more self-R&D and less R&D on trust than the other firms.

Originality/value
The finding is novel and original in a sense that the authors showed for the first time at firm-level microdata evidence that there is an optimal pattern of organizing supply chains within a multinational firm.
FMECA-based maintenance planning through COPRAS-G and PSI
Authors: Pancholi Nilesh , Bhatt Mangal 
Published: March 2018

Purpose
The purpose of this paper is to investigate the extent at which the reliability of an aluminium wire rolling mill can be improved by ameliorating current control and maintenance practices.

Design/methodology/approach
The paper deals with the discrimination of the most critical components by substantial shop-floor failure data. The research work narrates a method for evaluating maintainability criticality index for each failure cause of identified critical components through two different MCDM approaches: one based on grey-complex proportional risk assessment (COPRAS-G) and the other based on preference section index (PSI).

Findings
The primary findings of this research work are to prioritize the maintenance activities by comparing results obtained through different failure analysis models. It is proposing improvements in the maintenance plan of critical components like bearings, gears and shafts of an aluminium wire rolling mill which are commonly representing the most critical components in a large range of industrial processes.

Research limitations/implications
The limitation of the proposed study is that the failure models may not represent failures due to the first instant every time as adequate of design as such components are not checked for a high failure rate.

Practical implications
The proposed study is an interdisciplinary work which will help to understand about the working lives of components and associated failures. It will lead to reengineer new tools efficiently and to gain the maintenance excellence.

Originality/value
Originality mainly consists in the contemporary application of two non-identical MCDM-based methods (COPRAS-G and PSI). It will help to elucidate maintenance issues of major process industries and recommended deliverable keys.
Maintenance management for transportation process in quarry industry
Authors: Rukijkanpanich Jittra , Pasuk Panit 
Published: March 2018

Purpose
The purpose of this paper is to enhance the capability in managing the maintenance of the transportation process from a quarry to a crushing plant, measured by the availability value and the process capability value.

Design/methodology/approach
The maintenance management plan consists of plans for three levels of management: strategy, tactical and operational maintenance plans. The Deming cycle is a continuous improvement tool use for controlling and monitoring activities of the plans. There are three Deming cycles according to these plans, the first of which involves the improvement of machine performance and investment evaluation. The second involves the improvement of plans, schedule, and activities of preventive maintenance including autonomous maintenance. The third is for human resource development on maintenance works. Moreover, the feedback of a prior round of each cycle comes early to detect abnormalities that provide better capability in maintenance.

Findings
Three Deming cycles can use for enhancing the maintenance management. The parameters are availability (A) of machines and the capability process (Cpk) of the transportation process. The results of this research state that the availability value of machines increases to 80-92 percent while the process capability value increases to 0.56.

Practical implications
The maintenance management, especially strategic plan, tactical plan and operational plan via the Deming cycle, can be implemented in other medium-sized industries with limited technology and personnel. It was found that the implementation of the plans has continued to progress with the Deming cycle.

Originality/value
This paper proposes how to successfully implement the maintenance management for medium-sized industries with limited technology and personnel. The maintenance management of three levels is carried out simultaneously by using the Deming cycle. This work has proven to be successful which can be expressed in the availability and the capability process values.
Dependability-based maintenance optimization in healthcare domain
Authors: Mahfoud Hassana , Abdellah El Barkany , El Biyaali Ahmed 
Published: March 2018

PurposeThe purpose of this paper is to review maintenance strategies within the healthcare domain and to discuss practical needs as gaps between research and practice.Design/methodology/approachThe paper systematically categorizes the published literature on clinical maintenance optimization and then synthesizes it methodically.FindingsThis study highlights the significant issues relevant to the application of dependability analysis in healthcare maintenance, including the quantitative and qualitative criteria taken into account, data collection techniques and applied approaches to find the solution. Within each category, the gaps and further research needs have been discussed with respect to both an academic and industrial perspective.Practical implicationsIt is worth mentioning that medical devices are becoming more and more numerous, various and complex. Although, they are often affected by environmental disturbances, sharp technological development, stochastic and uncertain nature of operations and degradation and the integrity and interoperability of the supportability system, the associated practices related to asset management and maintenance in healthcare are still lacking. Therefore, the literature review of applied based research on maintenance subject is necessary to reveal the holistic issues and interrelationships of what has been published as categorized specific topics.Originality/valueThe paper presents a comprehensive review that will be useful to understand the maintenance problem and solution space within the healthcare context.
Reproductive ecology of three rareNorthAmericanPinguiculaspecies
Authors: Molano‐Flores Brenda , Primer Samantha , Annis Jenna , Feist Mary Ann , Coons Janice , Digges Roger 
Published: March 2018

AbstractPinguicula(Lentibulariaceae) is a genus of more than 100 carnivorous plant species. A handful of comprehensive studies have examined the reproductive ecology of these species, mostly in Europe and none in the USA. During 2013–2016 different aspects of the reproductive ecology ofP. ionantha,P. luteaandP. planifoliawere studied at multiple locations in the Florida Panhandle, USA. All three species are of conservation concern within the study region and some aspects of their reproductive ecology may be contributing to their rarity. For all species, we conducted breeding system studies investigating xenogamy vs. autogamy, self‐incompatibility vs. self‐compatibility, pollen:ovule ratios, flower phenology and longevity, and pollinator visitation, as well as fruit and seed set differences among populations. All threePinguiculaspecies were determined to be xenogamous and self‐compatible, although the pollen:ovule ratios were extremely low. In addition, these species have floral nastic movements and flower longevity that ranges from 2 to 3 weeks depending on the species. Hymenoptera was identified as the primary group of pollinators visiting all species, although observed visitation events were low. All threePinguiculaspecies had extremely high levels of fruit set and seed set. Worldwide,Pinguiculaspecies share similar breeding system and reproductive patterns. The rare status ofP. ionantha,P. luteaandP. planifoliais more likely due to their ecological requirements, demographics and/or patterns of genetic diversity, than reproduction. This work is among the first and most comprehensive associated with the reproductive ecology of North AmericanPinguicula.