bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energetics and Electronic Structure of h-BN Nanoflakes
Authors: Yamanaka Ayaka , Okada Susumu 
Published: August 2016

AbstractWe studied the energetics and electronic structure of hexagonal boron nitride (h-BN) nanoribbons with hydrogenated and clean edges with respect to the detailed edge shapes using density functional theory. Our calculations showed that the stability of h-BN edges strongly depends on the edge termination. In the case of hydrogenated edges, the formation energy is constant for all edge angles ranging from armchair to zigzag, indicating that h-BN may exhibit rich variation in their edge atomic arrangements under static conditions. The hydrogenated h-BN nanoribbons are insulators with an energy gap of 4 eV irrespective of edge shape, in which the lowest branch of the conduction band exhibits nearly free electron states nature distributed in the vacuum region outside the ribbons. In contrast, the formation energy of h-BN nanoribbons with clean edges monotonically increases as the edge angle is changed from armchair to zigzag. Our analysis reveals that the increase of density of states at the Fermi level arising from dangling bond states leads to this monotonic increase of edge formation energy in h-BN nanoribbons with clean edges.
Cell-cycle-controlled radiation therapy was effective for treating a murine malignant melanoma cell line in vitro and in vivo
Authors: Otani Keisuke , Naito Yoko , Sakaguchi Yukako , Seo Yuji , Takahashi Yutaka , Kikuta Junichi , Ogawa Kazuhiko , Ishii Masaru 
Published: August 2016

AbstractRadiotherapy is a commonly used regimen for treating various types of intractable cancers, although the effects depend on the cell cycle of the targeted cancer cell lines, and for irradiation purposes it is therefore critical to establish a protocol for controlling the cell cycle. Here, we showed that a common murine melanoma cell line B16BL6 was more vulnerable to irradiation during the early S phase, and that synchronisation of the cell cycle greatly increased the therapeutic effects of radiotherapy. Cell-sorting experiments, according to cell-cycle phase, using B16BL6 cells demonstrated that cells in the early S phase were the most susceptible to radiotherapy. Gemcitabine, a clinically utilised anti-cancer drug, induced cell-cycle arrest during the early S phase in B16BL6 cells, and thus a synergistic therapeutic effect was observed when irradiation was administered at the right time. Human pancreatic cancer cell line PANC-1 exhibited similar properties to B16BL6 in terms of its radiosensitivity during the S/G2/M phase and also demonstrated a synergistic effect of cell cycle synchronisation. These results show the importance of cell-cycle control in the application of irradiation and suggest a suitable time interval between chemotherapy and radiotherapy, as well as providing useful information for treating intractable cancer.
Serum metabonomics of acute leukemia using nuclear magnetic resonance spectroscopy
Authors: Musharraf Syed Ghulam , Siddiqui Amna Jabbar , Shamsi Tahir , Choudhary M. Iqbal , Rahman Atta-ur 
Published: August 2016

AbstractAcute leukemia is a critical neoplasm of white blood cells. In order to differentiate between the metabolic alterations associated with two subtypes of acute leukemia, acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML), we investigated the serum of ALL and AML patients and compared with two controls (healthy and aplastic anemia) using 1H NMR (nuclear magnetic resonance) spectroscopy. Thirty-seven putative metabolites were identified using Carr-Purcell-Meiboom-Gill (CPMG) sequence. The use of PLS-DA and OPLS-DA models gave results with 84.38% and 90.63% classification rate, respectively. The metabolites responsible for classification are mainly lipids, lactate and glucose. Compared with controls, ALL and AML patients showed serum metabonomic differences involving aberrant metabolism pathways including glycolysis, TCA cycle, lipoprotein changes, choline and fatty acid metabolisms.
Essential role of the nuclear isoform of RBFOX1, a candidate gene for autism spectrum disorders, in the brain development
Authors: Hamada Nanako , Ito Hidenori , Nishijo Takuma , Iwamoto Ikuko , Morishita Rika , Tabata Hidenori , Momiyama Toshihiko , Nagata Koh-Ichi 
Published: August 2016

AbstractGene abnormalities in RBFOX1, encoding an mRNA-splicing factor, have been shown to cause autism spectrum disorder and other neurodevelopmental disorders. Since pathophysiological significance of the dominant nuclear isoform in neurons, RBFOX1-isoform1 (iso1), remains to be elucidated, we performed comprehensive analyses of Rbfox1-iso1 during mouse corticogenesis. Knockdown of Rbfox1-iso1 by in utero electroporation caused abnormal neuronal positioning during corticogenesis, which was attributed to impaired migration. The defects were found to occur during radial migration and terminal translocation, perhaps due to impaired nucleokinesis. Axon extension and dendritic arborization were also suppressed in vivo in Rbfox1-iso1-deficient cortical neurons. In addition, electrophysiology experiments revealed significant defects in the membrane and synaptic properties of the deficient neurons. Aberrant morphology was further confirmed by in vitro analyses; Rbfox1-iso1-konckdown in hippocampal neurons resulted in the reduction of primary axon length, total length of dendrites, spine density and mature spine number. Taken together, this study shows that Rbfox1-iso1 plays an important role in neuronal migration and synapse network formation during corticogenesis. Defects in these critical processes may induce structural and functional defects in cortical neurons, and consequently contribute to the pathophysiology of neurodevelopmental disorders with RBFOX1 abnormalities.
Slow motion increases perceived intent
Authors: Caruso Eugene M. , Burns Zachary C. , Converse Benjamin A. 
Published: August 2016

Significance
When determining responsibility for harmful actions, people often consider whether the actor behaved intentionally. The spread of surveillance cameras, “on-officer” recording devices, and smart-phone video makes it increasingly likely that such judgments are aided by video replay. Yet, little is known about how different qualities of the video, such as replay speed, affect human judgment. We demonstrate that slow motion replay can systematically increase judgments of intent because it gives viewers the false impression that the actor had more time to premeditate before acting. In legal proceedings, these judgments of intent can mean the difference between life and death. Thus, any benefits of video replay should be weighed against its potentially biasing effects.
Physical coupling of activation and derepression activities to maintain an active transcriptional state at
FLC
Authors: Yang Hongchun , Howard Martin , Dean Caroline 
Published: August 2016

Significance
How chromatin influences transcription is a major question in biology. Chromatin states and transcriptional activity are correlated, but the interconnections and feedbacks in chromatin regulation that lead to quantitative transcriptional regulation are poorly understood. Previous mathematical modeling has shown the importance of dynamic, opposing histone modifications to enable maintenance of one chromatin state through many cell divisions, yet retain the ability to switch from one state to the other. Here, we validate a prediction of that modeling—physical association between the histone modifiers: the methyltransferase specific for the active state with the demethylase specific for the silent state. Such physical coupling of activities regulating opposing chromatin states is likely to be a general feature in chromatin-based transcriptional regulation.
On the solution of the Helmholtz equation on regions with corners
Authors: Serkh Kirill , Rokhlin Vladimir 
Published: August 2016

Significance
The solution of elliptic partial differential equations on regions with corners is a famously refractory problem. The solutions are known to be singular at corners, and one of the major difficulties has been finding a precise description of their behavior. In this paper, we observe that when the Helmholtz equation is solved using integral equations, the solutions are explicitly representable by certain series of known singular functions (in particular, Bessel functions of noninteger order). These explicit representations lead to highly accurate and efficient numerical algorithms for the solution of the Helmholtz equation on domains with corners.
Effect of Habitat Size, Quality, and Isolation on Functional Groups of Beetles in Hollow Oaks
Authors: Pilskog Hanne Eik , Birkemoe Tone , Framstad Erik , Sverdrup-Thygeson Anne 
Published: August 2016

Abstract
One of the largest threats to biodiversity is land use change and habitat loss. Hollow oaks (Quercus spp. L.) are well-defined patches that are hotspots for biodiversity and red-listed species, but they are often rare and fragmented in the landscape. We investigated the effect of patch size, habitat quality, and isolation on functional groups and red-listed saproxylic beetles in hollow oaks (n = 40) in Norway. The groups were defined by host tree association, trophic grouping, and red-listed status. Habitat quality, represented by tree form was most important in explaining species richness for most groups. Patch size, represented by circumference and amount of dead branches, was most important in explaining abundance. Isolation, that is single oaks compared with oaks in groups, had a negative effect on the abundance of beetles feeding both on wood and fungi (xylomycethopagous), as well as on species associated with broadleaved trees (oak semi-specialists), but did not affect species richness. This indicates that at this scale and in this landscape, isolated oaks are as species rich and valuable for conservation as other oaks, although some functional groups may be more vulnerable to isolation than others. The red-listed species only responded to patch size, indicating that oaks with large circumference and many dead branches are especially important for red-listed species and for conservation.
Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue
Authors: Kang Jin-Ho , Campos Marcelo L , Zemelis-Durfee Starla , Al-Haddad Jameel M , Jones A Daniel , Telewski Frank W , Brandizzi Federica , Howe Gregg A 
Published: August 2016

AbstractTrichomes are epidermal structures that provide a first line of defense against arthropod herbivores. The recessive hairless (hl) mutation in tomato (Solanum lycopersicum L.) causes severe distortion of trichomes on all aerial tissues, impairs the accumulation of sesquiterpene and polyphenolic compounds in glandular trichomes, and compromises resistance to the specialist herbivore Manduca sexta. Here, we demonstrate that the tomato Hl gene encodes a subunit (SRA1) of the highly conserved WAVE regulatory complex that controls nucleation of actin filaments in a wide range of eukaryotic cells. The tomato SRA1 gene spans a 42-kb region containing both Solyc11g013280 and Solyc11g013290. The hl mutation corresponds to a complex 3-kb deletion that removes the last exon of the gene. Expression of a wild-type SRA1 cDNA in the hl mutant background restored normal trichome development, accumulation of glandular trichome-derived metabolites, and resistance to insect herbivory. These findings establish a role for SRA1 in the development of tomato trichomes and also implicate the actin-cytoskeleton network in cytosolic control of specialized metabolism for plant defense. We also show that the brittleness of hl mutant stems is associated with altered mechanical and cell morphological properties of stem tissue, and demonstrate that this defect is directly linked to the mutation in SRA1.
Imagining Sisyphus happy: DNA barcoding and the unnamed majority
Authors: Blaxter Mark 
Published: August 2016

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on ‘charismatic megabionts’: larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue ‘From DNA barcodes to biomes’.
A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring
Authors: Hajibabaei Mehrdad , Baird Donald J. , Fahner Nicole A. , Beiko Robert , Golding G. Brian 
Published: August 2016

Encompassing the breadth of biodiversity in biomonitoring programmes has been frustrated by an inability to simultaneously identify large numbers of species accurately and in a timely fashion. Biomonitoring infers the state of an ecosystem from samples collected and identified using the best available taxonomic knowledge. The advent of DNA barcoding has now given way to the extraction of bulk DNA from mixed samples of organisms in environmental samples through the development of high-throughput sequencing (HTS). This DNA metabarcoding approach allows an unprecedented view of the true breadth and depth of biodiversity, but its adoption poses two important challenges. First, bioinformatics techniques must simultaneously perform complex analyses of large datasets and translate the results of these analyses to a range of users. Second, the insights gained from HTS need to be amalgamated with concepts such as Linnaean taxonomy and indicator species, which are less comprehensive but more intuitive. It is clear that we are moving beyond proof-of-concept studies to address the challenge of implementation of this new approach for environmental monitoring and regulation. Interpreting Darwin's ‘tangled bank’ through a DNA lens is now a reality, but the question remains: how can this information be generated and used reliably, and how does it relate to accepted norms in ecosystem study?This article is part of the themed issue ‘From DNA barcodes to biomes’.
Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans
Authors: Speller Camilla , van den Hurk Youri , Charpentier Anne , Rodrigues Ana , Gardeisen Armelle , Wilkens Barbara , McGrath Krista , Rowsell Keri , Spindler Luke , Collins Matthew , Hofreiter Michael 
Published: August 2016

Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
Counting animal species with DNA barcodes: Canadian insects
Authors: Hebert Paul D. N. , Ratnasingham Sujeevan , Zakharov Evgeny V. , Telfer Angela C. , Levesque-Beaudin Valerie , Milton Megan A. , Pedersen Stephanie , Jannetta Paul , deWaard Jeremy R. 
Published: August 2016

Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
DNA barcoding and taxonomy: dark taxa and dark texts
Authors: Page Roderic D. M. 
Published: August 2016

Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline (‘dark texts’). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These ‘dark taxa’ hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global ‘digital dashboard’ to assess the extent to which biodiversity data are available online.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
Multilocus inference of species trees and DNA barcoding
Authors: Mallo Diego , Posada David 
Published: August 2016

The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue ‘From DNA barcodes to biomes’.
DNA barcoding in diverse educational settings: five case studies
Authors: Henter Heather J. , Imondi Ralph , James Karen , Spencer Diana , Steinke Dirk 
Published: August 2016

Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5–18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.
This article is part of the themed issue ‘From DNA barcodes to biomes’.