bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal diets overwhelm host species in shaping the gut microbiota of Yak and Tibetan sheep
Authors: Wei Xiaojuan , Cheng Fusheng , Shi Hongmei , Zhou Xuzheng , Li Bing , Wang Ling , Wang Weiwei , Zhang Jiyu 
Published: November 2018

AbstractHost genetics and environmental factors can both shaping composition of gut microbiota, yet which factors are more important is still under debating. Yak (Bos grunniens) and Tibetan sheep (Ovis aries) are very different from the size and genetics. Nomadic Tibetan people keep them as main livestock and feeding them with same grazing systems, which provide a good opportunity to study the effects of diet and host species on gut microbiome. We collected fecal samples from yaks and Tibetan sheeps at different seasons when they were feed with different diets. Illumina data showed that major bacterial phyla of both animals are Bacteroidetes and Firmicutes, which agree with the previous reports. And the season effect had a higher impact on the gut microbiota than that of host species, though the animals are taxonomically distinguished each other at subfamily level. Since that the animal grazing differently at different seasons, this study indicated that diet can trump the host genetics even at higher taxonomic level. This finding provides a cautionary note for the researchers to link host genetics to the composition and function of the gut microbiota.ImportanceYak and Tibetan sheep are very different from the size and genetics (from different sub-family). Nomadic Tibetan people keep them as main livestock and feeding them with same grazing systems, which provide a good opportunity to study the effects of diet and host species on the gut microbiota. Results indicated that diet can trump the host genetics even at higher taxonomic level. This finding provides a cautionary note for the researchers to link host genetics to the composition and function of the gut microbiota.
Decoding the reproductive system of the olive fruit fly,Bactrocera oleae
Authors: Gregoriou M-E , Reczko M , Tsoumani K.T , Mathiopoulos K.D 
Published: November 2018

AbstractA great deal of behavioral and molecular interactions between male and female insects takes place during insect reproduction. Here, we comprehensively analyze the reproductive system of the olive fruit fly. Specifically, transcriptomic and genomic analysis of the reproductive tissues from virgin and once mated insects were performed. Genes encoding proteins implicated in immune response, mucins, antigen 5 proteins, proteases inhibitors and proteins with putative secretory activity were identified. Comparison of the transcriptomes between virgin and mated insects resulted in the identification of genes that are up- or down-regulated after mating. In testes 106 genes were up-regulated and 344 genes were down-regulated, whereas in male accessory glands with ejaculatory bulb 1,607 genes were up-regulated and 384 genes were down-regulated in mated male insects. Respectively, in mated females 1,705 genes were up-regulated and 120 genes were down-regulated in mated insects. To get a deeper insight, the expression profiles of selected genes throughout sexual maturation for the male tissues and throughout different time points after mating for the female reproductive tissues were determined. Identification of genes that take part in the mating procedure not only gives an insight in the biology of the insects, but it could also help the identification of new target genes in order to disturb the reproductive success of the olive fly and thus develop alternative pest control method.
Functional Anatomy, Biomechanical Performance Capabilities and Potential Niche of StW 573: anAustralopithecusSkeleton (circa 3.67 Ma) From Sterkfontein Member 2, and its significance for The Last Common Ancestor of the African Apes and for Hominin Origins
Authors: Crompton Robin Huw , McClymont Juliet , Thorpe Susannah , Sellers William , Heaton Jason , Pickering Travis Rayne , Pataky Todd , Stratford Dominic , Carlson Kristian , Jashashvili Tea , Beaudet Amélie , Bruxelles Laurent , Goh Colleen , Kuman Kathleen , Clarke Ronald 
Published: November 2018

Abstract (300 words)StW 573, from Sterkfontein Member 2, dated ca 3.67 Ma, is by far the most complete skeleton of an australopith to date. Joint morphology is in many cases closely matched in available elements ofAustralopithecus anamensis(eg.proximal and distal tibial and humeral joint-surfaces) and there are also close similarities to features of the scapula, in particular, of KSD-VP-1/1A. afarensisfrom Woranso-Mille. The closest similarities are, however, to the partial skeleton of StW 431 from Sterkfontein Member 4. When considered together, both StW 573 and StW 431 express an hip joint morphology quite distinct from that ofA. africanusSts14, and a proximal femur of a presumedA. africanusfrom Jacovec Cavern at Sterkfontein, StW 598. This, and other evidence presented herein, suggests there are two pelvic girdle morphs at Sterkfontein, supporting Clarke (2013) in his recognition of a second species,A. prometheus,containing StW 573 and StW 431. StW 573 is the first hominid skeleton where limb proportions are known unequivocally. It demonstrates that some early hominins, at the time of formation of the Laetoli footprints (3.6 Ma), were large-bodied. with hindlimbs longer than forelimbs. Modelling studies on extant primates indicate that the intermembral index (IMI) of StW 573, low for a non-human great ape, would have substantially enhanced economy of bipedal walking over medium-to-long distances, but that it was still too high for effective walking while load-carrying. It would, however, have somewhat reduced the economy of horizontal climbing, but madeGorilla-like embracing of large tree-trunks less possible. Consideration of both ethnographic evidence from modern indigenous arboreal foragers and modern degeneracy theory cautions against prescriptive interpretations of hand- and foot-function, by confirming that both human-like upright bipedalism and functional capabilities of the hand and foot can be effective in short-distance arboreal locomotion.
Regulatory Changes in Pterin and Carotenoid Genes Underlie Balanced Color Polymorphisms in the Wall Lizard
Authors: Andrade Pedro , Pinho Catarina , de Lanuza Guillem Pérez i , Afonso Sandra , Brejcha Jindřich , Rubin Carl-Johan , Wallerman Ola , Pereira Paulo , Sabatino Stephen J. , Bellati Adriana , Pellitteri-Rosa Daniele , Bosakova Zuzana , Carretero Miguel A. , Feiner Nathalie , Marsik Petr , Paupério Francisco , Salvi Daniele , Soler Lucile , While Geoffrey M. , Uller Tobias , Font Enrique , Andersson Leif , Carneiro Miguel 
Published: November 2018

ABSTRACTReptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard, which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions, near genes associated with pterin (SPR) and carotenoid metabolism (BCO2), demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been co-opted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles and haplotype analysis revealed abundant trans-specific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.
High-throughput functional analysis of IncRNA core promoters elucidatesrules governing tissue-specificity
Authors: Mattioli Kaia , Volders Pieter-Jan , Gerhardinger Chiara , Lee James C. , Maass Philipp G. , Melé Marta , Rinn John L. 
Published: November 2018

AbstractTranscription initiates at both coding and non-coding genomic elements, including mRNA and long non-coding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each class has different expression profiles with lncRNAs and eRNAs being the most tissue-specific. How these complex differences in expression profiles and tissue-specificities are encoded in a single DNA sequence, however, remains unresolved. Here, we address this question using computational approaches and massively parallel reporter assays (MPRA) surveying hundreds of promoters and enhancers. We find that both divergent lncRNA and mRNA core promoters have higher capacities to drive transcription than non-divergent lncRNA and mRNA core promoters, respectively. Conversely, lincRNAs and eRNAs have lower capacities to drive transcription and are more tissue-specific than divergent genes. This higher tissue-specificity is strongly associated with having less complex TF motif profiles at the core promoter. We experimentally validated these findings by testing both engineered single-nucleotide deletions and human single-nucleotide polymorphisms (SNPs) in MPRA. In both cases, we observe that single nucleotides associated with many motifs are important drivers of promoter activity. Thus, we suggest that high TF motif density serves as a robust mechanism to increase promoter activity at the expense of tissue-specificity. Moreover, we find that 22% of common SNPs in core promoter regions have significant regulatory effects. Collectively, our findings show that high TF motif density provides redundancy and increases promoter activity at the expense of tissue specificity, suggesting that specificity of expression may be regulated by simplicity of motif usage.
Mountain lion genomes provide insights into genetic rescue of inbred populations
Authors: Saremi Nedda F. , Supple Megan A. , Byrne Ashley , Cahill James A. , Coutinho Luiz Lehmann , Dalén Love , Figueiró Henrique V. , Johnson Warren E. , Milne Heather J. , O’Brien Stephen J. , O’Connell Brendan , Onorato David P. , Riley Seth P.D. , Sikich Jeff A. , Stahler Daniel R. , Villela Priscilla Marqui Schmidt , Vollmers Christopher , Wayne Robert K. , Eizirik Eduardo , Corbett-Detig Russell B. , Green Richard E. , Wilmers Christopher C. , Shapiro Beth 
Published: November 2018

Introduction paragraph/AbstractAcross the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of resequenced individuals from across their geographic range. We found strong geographical structure and signatures of severe inbreeding in all North American populations. Tracts of homozygosity were rarely shared among populations, suggesting that assisted gene flow would restore local genetic diversity. However, the genome of an admixed Florida panther that descended from a translocated individual from Central America had surprisingly long tracts of homozygosity, indicating that genomic gains from translocation were quickly lost by local inbreeding. Thus, to sustain diversity, genetic rescue will need to occur at regular intervals, through repeated translocations or restoring landscape connectivity. Mountain lions provide a rare opportunity to examine the potential to restore diversity through genetic rescue, and to observe the long-term effects of translocation. Our methods and results provide a framework for genome-wide analyses that can be applied to the management of small and isolated populations.
Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling
Authors: Fukaya Keiichi , Murakami Hiroaki , Yoon Seokjin , Minami Kenji , Osada Yutaka , Yamamoto Satoshi , Masuda Reiji , Kasai Akihide , Miyashita Kazushi , Minamoto Toshifumi , Kondoh Michio 
Published: November 2018

AbstractWe propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may oﬀer a new avenue for population monitoring based on the fast, cost-eﬀective, and non-invasive sampling of genetic information.
Dopamine regulates the exploration-exploitation trade-off in rats
Authors: Cinotti François , Fresno Virginie , Aklil Nassim , Coutureau Etienne , Girard Benoît , Marchand Alain R. , Khamassi Mehdi 
Published: November 2018

AbstractIn a volatile environment where rewards are uncertain, successful performance requires a delicate balance between exploitation of the best option and exploration of alternative choices. It has theoretically been proposed that dopamine controls this exploration-exploitation trade-off, specifically that the higher the level of tonic dopamine, the more exploitation is favored. We demonstrate here that there is a formal relationship between the rescaling of dopamine positive reward prediction errors and the exploration-exploitation trade-off in simple non-stationary multi-armed bandit tasks. We further show in rats performing such a task that systemically antagonizing dopamine receptors greatly increases the number of random choices without affecting learning capacities. Simulations and comparison of a set of different computational models (an extended Q-learning model, a directed exploration model, and a meta-learning model) fitted on each individual confirm that, independently of the model, decreasing dopaminergic activity does not affect learning rate but is equivalent to an increase in exploration rate. This study shows that dopamine could adapt the exploration-exploitation trade-off in decision making when facing changing environmental contingencies.
A conserved motif of Porphyromonas Type IX secretion effectors C-terminal secretion signal specifies interactions with the PorKLMN core complex
Authors: Vincent Maxence S. , Chabalier Maïalène , Cascales Eric 
Published: November 2018

ABSTRACTThe Type IX secretion system (T9SS) is a versatile protein transport apparatus restricted to the Bacteroidetes phylum. This multiprotein complex enables secretion of a wide range of effectors, such as protein toxins, filamentous adhesins, enzymes or S-layer subunits. Once translocated in the periplasm through the Sec pathway, recognition and secretion of these cargo proteins rely on a conserved C-terminal domain referred as CTD. However, the precise route followed by the CTD substrates from the periplasm to the cell exterior is yet to be determined. Here we define the interaction network of five different CTDs from the oral pathogen Porphyromonas gingivalis with the PorKLMN T9SS trans-envelope complex. We show that these five CTDs interact with the inner membrane-anchored PorM and the PorN periplasmic proteins. We further determine the contribution of the PorM IgG-like periplasmic domains and CTD conserved motifs for PorM-CTD complex formation. These results showed that all five CTDs interact with the core complex in a similar manner, suggesting a conserved mechanism of substrate selection in the periplasm. Our results thus establish a first model of the path followed by the CTD substrates through the T9SS.
RISC: robust integration of single-cell RNA-seq datasets with different extents of cell cluster overlap
Authors: Liu Yang , Wang Tao , Zheng Deyou 
Published: November 2018

AbstractSingle cell RNA-seq (scRNA-seq) has remarkably advanced our understanding of cellular heterogeneity and dynamics in tissue development, diseases, and cancers. Integrated data analysis can often uncover molecular and cellular links among individual datasets and thus provide new biological insights, such as developmental relationship. Due to differences in experimental platforms and biological sample batches, the integration of multiple scRNA-seq datasets is challenging. To address this, we developed a novel computational method for robust integration of scRNA-seq (RISC) datasets using principal component regression (PCR). Because of the natural compatibility of eigenvectors between PCR model and dimension reduction, RISC can accurately integrate scRNA-seq datasets and avoid over-integration. Compared to existing software, RISC shows particular improvement in integrating datasets that contain cells of the same types (more accurately clusters) but at distinct functional states. To demonstrate the value of RISC in finding small groups of cells common between otherwise heterogenous datasets, we applied it to scRNA-seq datasets of normal and malignant cells and successfully identified small clusters of cells in healthy kidney tissues that may be related to the origin of renal tumors.
Association between strategic management accounting facets and organizational performance
Authors: Alamri Ahmad Mohammed 
Published: November 2018

PurposeThe purpose of this paper is to develop an extensive conceptualization of strategic management accounting (SMA) facets, as well as to explore the impact of these facets on both financial and non-financial measures of organizational performance (OP).Design/methodology/approachData are collected from 435 accounting managers working in Saudi companies listed in the Saudi Stock Exchange. The study applies hierarchical regression analysis to test the association between SMA facets and OP.FindingsThe results show that SMA facets significantly affect OP, assessed in the two major categories of financial and non-financial performance.Research limitations/implicationsThe dominance of companies listed in the Saudi Stock Exchange in the data set limits the generalizability of the findings.Practical implicationsThe present study supports the idea that companies can enhance their OP by adopting some facets of SMA such as the availability of appropriate structural arrangements, supportive resources, adequate information types and usages and good organizational climate.Originality/valueThe current study expands the conceptualization of SMA in light of organizational context as a set of facets to overcome the polarization found in the existing literature and explores their impact on OP, including non-financial performance, for which empirical evidence is still scant.
Difficulty in implementing continuous improvement – Rasch measurement analysis
Authors: Sanchez-Ruiz Lidia , Blanco Beatriz , Diaz Emma 
Published: November 2018

Purpose
The purpose of this paper is to define a general and common construct in order to measure the level of difficulty companies experience when they implement continuous improvement (CI). Additionally, a rank of barriers is obtained together with a rank of companies.

Design/methodology/approach
In order to achieve the objective, first, a literature review is carried out to specify the domain of the construct; second, a sample of items is selected; third a survey is carried out in companies that have already implemented CI initiatives, the results being thus limited to this population; fourth, measures are purified by analysing the reliability and validity of the measurements, and finally results are obtained. The Rasch measurement theory will be used to provide a new perspective on a mature research topic.

Findings
It can be concluded that a new valid construct has been defined together with a rank of CI barriers, being lack of time the main barrier. A rank of companies is also obtained which is a first step in the development of future research studies.

Practical implications
Managers are provided with a better understanding of the barriers that can obstruct CI implementation. Thus, the rank of CI barriers guides managers through the most common and important obstacles so that they will be able to plan better CI strategies. In addition, the rank of companies allows each company to undertake a benchmarking exercise.

Originality/value
This work proposes a new way of analysing the difficulty in implementing CI as a continuum, rather than as independent barriers. From a theoretical point of view, it defines a new construct and offers a rank of CI barriers together with a rank of companies based on their level of difficulty when implementing CI initiatives. This is something new, as previous studies were mainly focussed on the items side. From a practical point of view, this study offers the surveyed companies the opportunity to see how they are positioned with respect to the other companies. Moreover, this rank of companies is the foundation on which to develop further studies with a practical orientation in the future.
Method for automatic key concepts extraction
Authors: Desul Sudarsana , N. Madurai Meenachi , Venkatesh Thejas , Gunta Vijitha , R. Gowtham , Sai Baba Magapu 
Published: November 2018

Purpose
Ontology of a domain mainly consists of a set of concepts and their semantic relations. It is typically constructed and maintained by using ontology editors with substantial human intervention. It is desirable to perform the task automatically, which has led to the development of ontology learning techniques. One of the main challenges of ontology learning from the text is to identify key concepts from the documents. A wide range of techniques for key concept extraction have been proposed but are having the limitations of low accuracy, poor performance, not so flexible and applicability to a specific domain. The propose of this study is to explore a new method to extract key concepts and to apply them to literature in the nuclear domain.

Design/methodology/approach
In this article, a novel method for key concept extraction is proposed and applied to the documents from the nuclear domain. A hybrid approach was used, which includes a combination of domain, syntactic name entity knowledge and statistical based methods. The performance of the developed method has been evaluated from the data obtained using two out of three voting logic from three domain experts by using 120 documents retrieved from SCOPUS database.

Findings
The work reported pertains to extracting concepts from the set of selected documents and aids the search for documents relating to given concepts. The results of a case study indicated that the method developed has demonstrated better metrics than Text2Onto and CFinder. The method described has the capability of extracting valid key concepts from a set of candidates with long phrases.

Research limitations/implications
The present study is restricted to literature coming out in the English language and applied to the documents from nuclear domain. It has the potential to extend to other domains also.

Practical implications
The work carried out in the current study has the potential of leading to updating International Nuclear Information System thesaurus for ontology in the nuclear domain. This can lead to efficient search methods.

Originality/value
This work is the first attempt to automatically extract key concepts from the nuclear documents. The proposed approach will address and fix the most of the problems that are existed in the current methods and thereby increase the performance.