bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Expression Distribution Deconvolution in Single Cell RNA Sequencing
Authors: Wang Jingshu , Huang Mo , Torre Eduardo , Dueck Hannah , Shaffer Sydney , Murray John , Raj Arjun , Li Mingyao , Zhang Nancy R. 
Published: December 2017

AbstractSingle-cell RNA sequencing (scRNA-seq) enables the quantification of each gene’s expression distribution across cells, thus allowing the assessment of the dispersion, burstiness, and other aspects of its distribution beyond the mean. These statistical characterizations of the gene expression distribution are critical for understanding expression variation and for selecting marker genes for population heterogeneity. However, scRNA-seq data is noisy, with each cell typically sequenced at low coverage, thus making it difficult to infer properties of the gene expression distribution from raw counts. Based on a re-examination of 9 public data sets, we propose a simple technical noise model for scRNA-seq data with Unique Molecular Identifiers (UMI). We develop DESCEND, a method that deconvolves the true cross-cell gene expression distribution from observed scRNA-seq counts, leading to improved estimates of properties of the distribution such as dispersion and burstiness. DESCEND can adjust for cell-level covariates such as cell size, cell cycle and batch effects. DESCEND’s noise model and estimation accuracy are further evaluated through comparisons to RNA FISH data, through data splitting and simulations, and through its effectiveness in removing known batch effects. We demonstrate how DESCEND can clarify and improve downstream analyses such as finding differentially bursty genes, identifying cell types, and selecting differentiation markers.
The GCTx format and cmap{Py, R, M} packages: resources for the optimized storage and integrated traversal of dense matrices of data and annotations
Authors: Enache Oana M. , Lahr David L. , Natoli Ted E. , Litichevskiy Lev , Wadden David , Flynn Corey , Gould Joshua , Asiedu Jacob K. , Narayan Rajiv , Subramanian Aravind 
Published: December 2017

AbstractMotivationComputational analysis of datasets generated by treating cells with pharmacological and genetic perturbagens has proven useful for the discovery of functional relationships. Facilitated by technological improvements, perturbational datasets have grown in recent years to include millions of experiments. While initial studies, such as our work on Connectivity Map, used gene expression readouts, recent studies from the NIH LINCS consortium have expanded to a more diverse set of molecular readouts, including proteomic and cell morphological signatures. Sharing these diverse data creates many opportunities for research and discovery, but the unprecedented size of data generated and the complex metadata associated with experiments have also created fundamental technical challenges regarding data storage and cross-assay integration.ResultsWe present the GCTx file format and a suite of open-source packages for the efficient storage, serialization, and analysis of dense two-dimensional matrices. The utility of this format is not just theoretical; we have extensively used the format in the Connectivity Map to assemble and share massive data sets comprising 1.7 million experiments. We anticipate that the generalizability of the GCTx format, paired with code libraries that we provide, will stimulate wider adoption and lower barriers for integrated cross-assay analysis and algorithm development.AvailabilitySoftware packages (available in Matlab, Python, and R) are freely available athttps://github.com/cmapSupplementary informationSupplementary information is available at clue.io/code.Contactoana@broadinstitute.org
SNPTB: nucleotide variant identification and annotation in Mycobacterium tuberculosis genomes
Authors: Gupta Aditi 
Published: December 2017

AbstractSummaryWhole genome sequencing (WGS) has become a mainstay in biomedical research. The continually decreasing cost of sequencing has resulted in a data deluge that underlines the need for easy-to-use bioinformatics pipelines that can mine meaningful information from WGS data. SNPTB is one such pipeline that analyzes WGS data originating from in vitro or clinical samples of Mycobacterium tuberculosis and outputs high-confidence single nucleotide polymorphisms in the bacterial genome. The name of the mutated gene and the functional consequence of the mutation on the gene product is also determined. SNPTB utilizes open source software for WGS data analyses and is written primarily for biologists with minimal computational skills.Availability and implementationSNPTB is a python package and is available from https://github.com/aditi9783/SNPTBContactag1349@njms.rutgers.eduSupplementary informationTutorial for SNPTB is available at https://github.com/aditi9783/SNPTB/blob/master/docs/SNPTB_tutorial.md
The use of salivary α-amylase as an evolutionary solution to host selection in parasitoids
Authors: Bichang’a Gladys , Da Lage Jean-Luc , Mailhan Claire-Marie , Marion-Poll Frédéric , Capdevielle-Dulac Claire , Zivy Michel , Balliau Thierry , Ru Bruno Le , Kaiser-Arnauld Laure , Juma Gerald , Maina Esther , Calatayud Paul-andré 
Published: December 2017

AbstractForaging parasitoids use chemical signals in host recognition and selection processes. Thereby, chemicals from the herbivore hosts play a crucial role. When different herbivores are present in the same plant or field, the perception of specific volatiles and contact compounds emitted from the host itself enable the parasitoids both to differentiate between hosts and non-hosts and to estimate the health status of its host. During the host feeding process, contact between the parasitoid and its host is very crucial, and oral secretions from the host play a key role during the first contact for such evaluation by the parasitoid. Using an integration of behavioral observations, biochemical and sensory physiological approaches we demonstrate that female parasitoids of Cotesia flavipes recognize their host and oviposit in reaction to an α-amylase, which is present in the oral secretions of the larvae of their host, Chilo partellus. This activity was also mediated by a purified α-amylase synthetized from Drosophila melanogaster. Using this synthetized enzyme, we further demonstrate that the conformation of the enzyme rather than its catalytic site is responsible for this activity. This enzyme is activating gustatory neurons of the terminal antennal sensilla chaetica of C. flavipes females. α-amylases are therefore good candidates for an evolutionary solution to host selection in parasitoids, thus opening new avenues for investigations in hosts-parasitoids interactions.
Hybrid Songbirds are Deficient in Learning and Memory
Authors: McQuillan Michael A. , Roth Timothy C. , Huynh Alex V. , Rice Amber M. 
Published: December 2017

AbstractIdentifying the phenotypes underlying postzygotic reproductive isolation is crucial for fully understanding the evolution and maintenance of species. One potential postzygotic isolating barrier that has not yet been examined is learning and memory ability in hybrids. Learning and memory are important fitness-related traits, especially in scatter-hoarding species, where accurate retrieval of hoarded food is vital for winter survival. Here, we test the hypothesis that learning and memory ability can act as a postzygotic isolating barrier by comparing these traits among two scatter-hoarding songbird species, black-capped (Poecile atricapillus), Carolina chickadees (Poecile carolinensis), and their naturally occurring hybrids. In an outdoor aviary setting, we find that hybrid chickadees perform significantly worse on an associative learning spatial task and are worse at solving a novel problem compared to both parental species. Deficiencies in learning and memory abilities could therefore contribute to postzygotic reproductive isolation between chickadee species. Given the importance of learning and memory for fitness, our results suggest that these traits may play an important, but as yet overlooked, role in postzygotic reproductive isolation.
The interplay between facilitation and habitat type drive spatial vegetation patterns in global drylands
Authors: Berdugo Miguel , Soliveres Santiago , Kéfi Sonia , Maestre Fernando T. 
Published: December 2017

ABSTRACTThe size distribution of discrete plant patches (PSD), a common descriptor of the spatial patterns of vascular vegetation, has been linked to variations in land degradation and ecosystem functioning in drylands. However, most studies on PSDs conducted to date have focused on a single or a few study sites within a particular region. Therefore, little is know on the general typology and distribution of PSDs at the global scale, and on the relative importance of biotic and abiotic factors as drivers of their variation across geographical regions and habitat types. We analyzed 115 dryland plant communities from all continents except Antarctica to investigate the general typology of PSDs, and to assess the relative importance of biotic (plant cover, frequency of facilitation, soil amelioration, height of the dominant species) and abiotic (aridity and sand content) factors as drivers of PSDs across contrasting habitat types (shrublands and grasslands). We found that both power-law and lognormal PSDs were generally distributed regardless of the region of the world considered. The percentage of facilitated species in the community drives the emergence of power-law like spatial patterns in both shrublands and grasslands, although mediated by different mechanisms (soil and climatic amelioration, respectively). Other drivers of PSDs were habitat-specific: height of the dominant species and total cover were particularly strong drivers in shrublands and grasslands, respectively. The importance of biotic attributes as drivers of PSDs declined under the most arid conditions in both habitats. We observed that PSDs deviated from power law functions not only due to the loss of large, but also of small patches. Our results expand our knowledge about patch formation in drylands and the habitat-dependency of their drivers. They also highlight different ways in which facilitation may act on ecosystem functioning through the formation of plant spatial patterns.
Oxford Nanopore sequencing in a research-based undergraduate course
Authors: Zeng Yi , Martin Christopher H. 
Published: December 2017

AbstractBackgroundNanopore sequencing is a third generation genomic sequencing method that offers real time sequencing of DNA samples. Nanopore sequencing is an excellent tool for teaching because it involves cutting-edge sequencing methods and also helps students to develop a research mindset, where students can learn to identify and resolve problems that arise during an experiment.ResultsWe, as a group of undergraduate biology students, were able to use nanopore sequencing to analyze a sample of pupfish DNA. We were able to accomplish this without computer science backgrounds and only some basic DNA extraction training. Although there were issues, such as inconsistent results across runs, we found it useful as a research learning experience and an application of the skills we learned.ConclusionsAs students, it was exciting to be able to experience this technology first hand and apply what we learned in the classroom. Nanopore sequencing holds potential for DNA sequencing of large fragments in real time. It allows students to be acquainted with novel technologies and the theories behind them. However, as with all new techniques, it does not have the same established support, and when students run into difficulties while using nanopore sequencing, it is often difficult to identify what went wrong.
Root endophytic Chaetomium cupreum promotes plant growth and detoxifies aluminum in Miscanthus sinensisAndersson growing at the acidic mine site
Authors: Haruma Toshikatsu , Yamaji Keiko , Masuya Hayato , Hanyu Kazuyo 
Published: December 2017

Abstract
Miscanthus sinensis Andersson grows naturally at the Hitachi mine. The root‐zone soil was acidic and contained high concentrations of Cu, Pb, Zn and exchangeable Al. Adventitious roots accumulated high concentrations of Al and Fe, but not other heavy metals. The purpose of this study was to elucidate the mechanism of tolerance of Al in M. sinensis, focusing on its chemical interaction with root endophytes. We isolated Chaetomium cupreum, which produced siderophores, from adventitious roots of M. sinensis via CAS assay. In inoculation tests, C. cupreum promoted M. sinensis seedling growth and increased Al and Fe uptake in the roots, although C. cupreum did not stimulate M. sinensis to produce Al detoxicants, such as citric and malic acids. Observation of the pattern of Al localization in the roots clarified that C. cupreum reduced Al toxicity in M. sinensis via compartmentalizing Al into fungal mycelia surrounding the roots and creating a less toxic Al‐localization pattern, allocating Al to the epidermis, endodermis and stele of roots. In conclusion, our results indicated that C. cupreum increases Al tolerance in M. sinensis growing at the acidic mine site.
Assessing the Association between Trust and Concentration Area of Migrant Ethnic Minority in Sydney
Authors: Vidyattama Yogi 
Published: December 2017

AbstractThere is ongoing concern that concentrations of migrant ethnic minority groups could increase distrust within Australian communities. This article assesses whether the existence of an area of high migrant ethnic minority concentration associates with low propensity to trust. After identification using Local Spatial Autocorrelation Statistics and controlling for other variables, a regression technique indicated significantly low trust associated with this area in 2006. Further investigation shows that the association of low level of trust and the concentration area was not as severe in 2010 and had even smaller and insignificant association in 2005.
Alternative Distributions for Inequality Comparisons
Authors: Creedy John 
Published: December 2017

AbstractThis article provides an introductory review of the alternative possible income distributions that can be used when making cross‐sectional evaluations of inequality changes and the effects of taxes and transfers using a household economic survey. It attempts to clarify the various alternatives for users of data and those interpreting results. It focuses on the choice of income unit and the need to avoid spurious comparisons. The use of adult equivalence scales and the application of an explicit sharing rule are considered, as are comparisons over time where the tax structure and populations differ. Numerical examples highlight the alternative approaches and distributions.
Structural Reform for Economic Growth
Authors: Cai Fang , Zhang Xiaojing 
Published: December 2017

AbstractThis article examines the role of reform in maintaining economic growth in the circumstances in which work‐age is declining more rapidly than total population. Traditional factor‐driven growth can still contribute if reform increases labour force participation, most significantly through easing restrictions on rural–urban migration through reform of the household registration system and other means. The other potential contributor to growth in the new era is reform to raise productivity. This requires more fundamental institutional change, which depends on clear visions of the framework for a modern market economy, encompassing the rule of law and stronger property rights.
China's Macroeconomic Balancing Act: Shifting to New Drivers of Growth and Sustaining Financial Stability
Authors: Huang Yiping , Shen Yan , Fu Qiuzi 
Published: December 2017

AbstractIn the lead‐up to China's five‐yearly National Party Congress late in 2017, attempts to resolve conflicts between short‐term growth and structural reform have tended to favour immediate growth. The new model of growth requires new economy sectors to grow much more rapidly than traditional (post‐1978) sectors. For a while, this was proceeding well, but in late 2016 and during 2017 there have been signs of priority for growth and therefore traditional sectors over the new economy. Favouring growth over reform introduces risk into longer‐term growth prospects.
A new Nabataean funerary inscription from Dhībān, with a brief account on Dhībān during the Nabataean period
Authors: al‐Salameen Zeyad , Al‐Rawahneh Musallam 
Published: December 2017

AbstractThis paper investigates a two‐line unpublished Nabataean funerary inscription found in 2016 at Dhībān, 70 km south of Amman. The inscription, which is the first known Nabataean text from this site, represents a dedication of a funerary monument, a nefesh, by a person to his deceased son. The current study includes a word‐by‐word discussion of the text, offering remarks on its discovery as well as a linguistic analysis of its contents. A brief account of the Nabataean occupation at Dhībān is also provided.
The Taymanitic onomasticon
Authors: Kootstra F. 
Published: December 2017

AbstractThe Taymanitic inscriptions, written in the c. mid‐sixth century BCE, largely consist of personal names. While personal names cannot inform us directly on the language or ethnicity of their bearers, name‐giving practices do reflect a choice made by the person bestowing it on someone. This article will focus on the personal names of the inscriptions; what they can tell us about their linguistic and cultural background, and how this might inform us on the cultural heritage of the authors of the Taymanitic inscriptions.
Large Kombewa flake production in north Oman
Authors: Beshkani Amir , Beuzen‐Waller Tara , Bonilauri Stéphanie , Gernez Guillaume 
Published: December 2017

AbstractIn this paper we present the results of surveys carried out in February 2016 along a palaeo‐drainage system near the village of Bisyah. We report first on the geological prospection, which was our main goal, and then present our discovery of the only known localities in north Oman of large Kombewa flake production (>10 cm up to 20 cm). Among the scatter of artefacts, we found cores and large Kombewa flakes with two opposed bulbs of percussion, a technology that had not been known in this region until now. In spite of the local features, the typo‐technological traits of the artefacts suggest that at least part of them resemble in some way the Acheulean techno‐complex, but there are still many questions remaining on the age of these artefacts.
Dorsal surgical stabilisation using tension bands for treatment of traumatic atlanto‐occipital instability in a cat
Authors: Vedrine B , Maurin MP 
Published: December 2017

Case reportAn atlanto‐occipital instability secondary to a dog bite was diagnosed in a 4‐year‐old Persian cat. Dorsal stabilisation of the instability was made with two OrthoFiber prostheses (Securos), which were used as tension bands between the nuchal crests of the occipital bone and the spinous process of the axis. Total recovery was achieved 4 days after surgery. Normal alignment of the atlanto‐occipital joint was observed on survey radiographs taken 6 weeks post‐surgery. Although the right loop had failed, the alignment was still normal and no neurological after‐effects could be identified.ConclusionDorsal divergent tension bands between the nuchal crests of the occipital bone and the spinous process of the axis can be used to stabilise traumatic atlanto‐occipital instability.
The vestiges and vanguards of policy design in a digital context
Authors: Clarke Amanda , Craft Jonathan 
Published: December 2017

AbstractThis article explores the opportunities, challenges and expectations that the digital context of design and new digital era policy instruments, such as open data, big data, robotics and crowdsourcing, present to policy designers operating in today's governments. Adopting an instruments perspective, the article identifies four characteristics of digital era policy design before detailing three issues that must be addressed to ascertain the promise and pitfalls of digital era policy design. First, we argue that scholars and practitioners alike must investigate how traditional constraints on the ideal of rational, evidence‐driven policy design—long acknowledged in the “analogue design” literature—will fade or be exacerbated in the digital age. The article next confronts the reality that new digital designs and instruments will rarely emerge in a policy vacuum, but rather will be layered onto existing policy designs and complex policy mixes with sticky legacies that will be more or less amenable to digital design approaches. Finally, the article argues that while scholars and practitioners have been quick to presume that the digital age will foster a more collaborative model of state‐to‐non‐state cooperation, digital era policy design may ultimately marginalize or eliminate citizens altogether from the design process, raising important questions about the as of yet little understood democratic implications of digital era policy design.
The evolution of citizen and stakeholder engagement in Canada, from Spicer to #Hashtags
Authors: Longo Justin 
Published: December 2017

AbstractGovernment‐led citizen and stakeholder engagement is undertaken with the broad aims of improving government effectiveness and strengthening perceived legitimacy for government action. However, some aspects of the digital era that are challenging and stretching these traditions include changing economics of attention, heightened expectations of citizens and stakeholders, and a reconfiguration of the nature of policymaking discourse. Seven Government of Canada citizen and stakeholder engagement cases, spread over the past 27 years, are reviewed against the emergence of digital technologies within the context of traditional engagement exercises to understand how governments are experimenting with new approaches, and how new models may still be needed to respond to this shifting technology landscape. A future research agenda is sketched that anticipates how expanding technological capabilities, changing expectations on the part of citizens and stakeholders, and new approaches to policy discourse might require a reappraisal of our concepts of citizen and stakeholder engagement.