bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using microscopy and DNA metabarcoding
Authors: Macgregor Callum J. , Kitson James J.N. , Fox Richard , Hahn Christoph , Lunt David H. , Pocock Michael J.O. , Evans Darren M. 
Published: May 2018

AbstractMoths are globally relevant as pollinators but nocturnal pollination remains poorly understood. Plant-pollinator interaction networks are traditionally constructed using either flower-visitor observations or pollen-transport detection using microscopy. Recent studies have shown the potential of DNA metabarcoding for detecting and identifying pollen-transport interactions. However, no study has directly compared the realised observations of pollen-transport networks between DNA metabarcoding and conventional light microscopy.Using matched samples of nocturnal moths, we construct pollen-transport networks using two methods: light microscopy and DNA metabarcoding. Focussing on the feeding mouthparts of moths, we develop and provide reproducible methods for merging DNA metabarcoding and ecological network analysis to better understand species-interactions.DNA metabarcoding detected pollen on more individual moths, and detected multiple pollen types on more individuals than microscopy, but the average number of pollen types per individual was unchanged. However, after aggregating individuals of each species, metabarcoding detected more interactions per moth species. Pollen-transport network metrics differed between methods, because of variation in the ability of each to detect multiple pollen types per moth and to separate morphologically-similar or related pollen. We detected unexpected but plausible moth-plant interactions with metabarcoding, revealing new detail about nocturnal pollination systems.The nocturnal pollination networks observed using metabarcoding and microscopy were similar, yet distinct, with implications for network ecologists. Comparisons between networks constructed using metabarcoding and traditional methods should therefore be treated with caution. Nevertheless, the potential applications of metabarcoding for studying plant-pollinator interaction networks are encouraging, especially when investigating understudied pollinators such as moths.
S-MiRAGE: A quantitative, secreted RNA-based reporter of gene expression and cell persistence
Authors: Mitra Kinshuk , Feist William N. , Anfossi Simone , Fuentes-Mattei Enrique , Almeida Maria Ines , Kim Jean J. , Calin George A. , Warmflash Aryeh 
Published: May 2018

AbstractNon-destructive measurements of cell persistence and gene expression are crucial for longitudinal research studies and for prognostic assessment of cell therapies. Here we describe S-MiRAGE, a platform that utilizes small secreted RNA molecules as sensitive and quantitatively accurate reporters of cellular processes. We demonstrate the utility of S-MiRAGE by monitoring the differentiation status of human embryonic stem cells in vitro, and tumor growth in a mouse model in vivo.
A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marineSynechococcus‘relic’ prophage
Authors: Flores-Uribe José , Philosof Alon , Sharon Itai , Fridman Svetlana , Larom Shirley , Béjà Oded 
Published: May 2018

SummaryMarine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea andTaraOceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.Originality-Significance StatementMarine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island inSynechococcusWH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured cyanophage but shares several genes with the newly identified cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.
Theaflavins, polyphenols of black tea, inhibit entry of hepatitis C virus
Authors: Chowdhury Pritom , Sahuc Marie-Emmanuelle , Rouillé Yves , Vandeputte Alexandre , Brodin Priscille , Goswami Manoranjan , Bandyopadhyay Tanoy , Dubuisson Jean , Séron Karin 
Published: May 2018

AbstractThe treatment of hepatitis C virus (HCV) infection by combination of direct acting antivirals (DAA), with different mode of action, has made substantial progress in the past few years. However, appearance of resistance and high cost of the therapy is still an obstacle in the achievement of the therapy, more specifically in developing countries. In this context, search for affordable antivirals with new mechanisms of action is still needed. Tea, after water, is the most popular drink worldwide. Polyphenols extracted from green tea have already shown anti-HCV activity as entry inhibitors. Here, three different theaflavins, theaflavin (TF1), theaflavin-3’-monogallate (TF2), and theaflavin-3-3’-digallate (TF3), which are major polyphenols from black tea, were tested against HCV in cell culture. The results showed that all theaflavins inhibit HCV infection in a dose-dependent manner in an early step of infection. Results obtained with HCV pseudotyped virions confirmed their activity on HCV entry and demonstrated their pan-genotypic action. No effect on HCV replication was observed by using HCV replicon. Investigation on the mechanism of action of black tea theaflavins showed that they act directly on the virus particle and are able to inhibit cell-to-cell spread. Combination study with inhibitors most widely used in anti-HCV treatment regimen demonstrated that TF3 exerts additive effect. In conclusion, theaflavins, that are present in high quantity in black tea, are new inhibitors of HCV entry and hold promise for developing in therapeutic arsenal for HCV infection.
Unprecedented account of mortality and morbidity in free ranging Formosan Pangolin (Manis pentadactyla pentadactyla)
Authors: Sun Nick Ching-Min , Arora Bharti , Lin Jing-Shiun , Lin Wen-Chi , Chi Meng-Jou , Chen Chen-Chih , Pei Kurtis Jai-Chyi 
Published: May 2018

AbstractGlobally, pangolins are overt for poaching and illegal trade, but Taiwan projects totally a contrary image where their population is stable and increasing. This paper illustrated the factors responsible for causing mortality and morbidity in free ranging Formosan pangolin (M. pentadactyla pentadactyla). Results from radio-tracking showed that Formosan pangolins are highly susceptible to stuck in tree hallows or ground burrows despite being proficient burrowers, and killed by gin traps, especially during the dryer season. Whilst the data consolidated from the Pingtung Rescue Center for Endangered Wild Animals illustrated the trauma (73.0%) was the major reason of causing morbidity in Formosan pangolin. The gin traps were the leading cause of trauma (77.8%) along with tail injuries caused by dog attack (20.4%). Despite all the pressing data about the injuries Taiwan, it is able to establish substantial success rate in rescuing and releasing pangolins through consolidating and applying valuable information among the rescue centers in the span of two decades. Taiwan has made a phenomenal progress in sustaining a salubrious population of pangolin but the situation requires continuous examination to ensure the existence of this species on the island.
Hormonal signaling cascades required for phototaxis switch in wanderingLeptinotarsa decemlineatalarvae
Authors: Meng Qing-Wei , Xu Qing-Yu , Zhu Tao-Tao , Jin Lin , Fu Kai-Yun , Guo Wen-Chao , Li Guo-Qing 
Published: May 2018

AbstractMany animals exploit several niches sequentially during their life cycles, a fitness referred to as ontogenetic niche shift (ONS). To successfully accomplish ONS, transition between development stages is often coupled with changes in one or more primitive, instinctive behaviors. Yet, the underlining molecular mechanisms remain elusive. We show here thatLeptinotarsa decemlineatalarvae finish their ONS at the wandering stage by leaving the plant and pupating in soil. At middle wandering phase, larvae also switch their phototactic behavior, from photophilic at foraging period to photophobic. We find that enhancement of juvenile hormone (JH) signal delays the phototactic switch, andvise verse. Moreover, RNA interference (RNAi)-aided knockdown ofLdPTTH(prothoracicotropic hormone gene) orLdTorso(PTTH receptor gene) impairs avoidance response to light, a phenotype nonrescuable by 20-hydroxyecdysone. Consequently, the RNAi beetles pupate at the soil surface or in shallow layer of soil, with most of them failing to construct pupation chambers. Furthermore, a combination of depletion ofLdPTTH/LdTorsoand disturbance of JH signal causes no additional effects on light avoidance response and pupation site. Finally, we establish that TrpA1 (transient receptor potential (TRP) cation channel) is necessary for light avoidance behavior, acting downstream of PTTH. We conclude that JH/PTTH cascade concomitantly regulates metamorphosis and the phototaxis switch, to drive ONS of the wandering beetles from plant into soil to start the immobile pupal stage.Author summaryMany animals occupy distinct niches and utilize diverse resources at different development stages in order to meet stage-dependent requirements and overcome stage-specific limitations. This fitness is referred to as ontogenetic niche shift (ONS). During the preparation for ONS, animals often change one or more primitive, instinctive behaviors. Holometabolous insects, with four discrete developmental periods usually in different niches, are a suitable animal group to explore the molecular modes of these behavioral switches. Here we find thatLeptinotarsa decemlineatalarvae, an insect defoliator of potatoes, switch their phototactic behavior, from photophilic at feeding period to photophobic during the larval-pupal transition (wandering stage). This phototactic switch facilitates the wandering larvae to accomplish the ONS from potato plant to their pupation site below ground. We show that JH/PTTH cascade controls the phototaxis switch, through a step in photo transduction between the photoreceptor molecule and the transient receptor potential cation channel.
Messenger RNAs transcribed from yeast linear cytoplasmic plasmids possess unconventional 5’ and 3’ UTRs and suggest a novel mechanism of translation
Authors: Vopálenský Václav , Sýkora Michal , Mašek Tomáš , Pospíšek Martin 
Published: May 2018

AbstractLinear plasmids with almost identical compact genetic organization have been found in the cytoplasm of yeast species from nine genera. We employed pGKL1,2 plasmids fromKluyveromyces lactisas a model to investigate the previously unstudied transcriptome of yeast cytoplasmic linear plasmids. We performed 5’ and 3’ RACE analysis of all the pGKL1,2 mRNAs and found them not 3’ polyadenylated and containing mostly uncapped 5’ poly(A) leaders that are not complementary to the plasmid DNA. The degree of 5’ capping and/or 5’ polyadenylation is specific to each gene and is controlled by the corresponding promoter regions. We refined the description of the pGKL1,2 promoters and found new alternative promoters of several genes. We also provide evidence thatK2ORF3encodes an mRNA cap guanine-N7-methyltransferase and that 5’ capped pGKL1,2 transcripts contain N7-methylated caps. Translation of pGKL1,2 transcripts is enhanced inIsm1Δandpab1Δstrains and is independent of eIF4E and Pab1 translation factors. We suggested a model of a primitive regulation of pGKL1,2 plasmids gene expression where degree of 5’ mRNA capping, degree of 5’ non-template polyadenylation and presence of negative regulators as PAB1 and Lsm1 play an important role. Our data also suggest a close relationship between linear plasmids and poxviruses.
Splicing and epigenetic factors jointly regulate epidermal differentiation
Authors: Tanis Sabine E.J. , Jansen Pascal W.T.C. , Zhou Huiqing , Vermeulen Michiel , Mulder Klaas W. 
Published: May 2018

AbstractEpidermal homeostasis requires a continuous balance between progenitor cell proliferation and loss of differentiated cells from its surface. During this process cells undergo major changes in their transcriptional programs to accommodate new cellular functions. We found that transcriptional and post-transcriptional mechanisms underlying these changes are functionally connected and jointly control genes involved in cell adhesion, a key process in epidermal maintenance. Using siRNA-based perturbation screens, we identified novel DNA/RNA binding regulators of epidermal differentiation. Computational modeling and experimental validation identified functional interactions between the matrin-type 2 zinc-finger protein ZMAT2 and the epigenetic modifiers ING5, SMARCA5, BRD1, UHRF1, BPTF, SMARCC2. ZMAT2 is required to keep cells in an undifferentiated, proliferative state and quantitative proteomics identified ZMAT2 as an interactor of the pre-spliceosome. RNA-Immunoprecipitation and transcriptome-wide RNA splicing analysis showed that ZMAT2 associates with and regulates transcripts involved in cell adhesion in conjuction with ING5. Thus, joint control by post-transcriptional and epigenetic mechanisms is important to maintain epidermal cells in an undifferentiated state.Highlights-Gene-perturbation screens identify a role for ZMAT2 in the control of human epidermal differentiation.-ZMAT2 functionally interacts with known epigenetic regulators of epidermal differentiation.-ZMAT2 interacts with the pre-spliceosome and transcripts involved in cell adhesion.-ZMAT2 mediated splicing and epigenetic control jointly target an adhesion related transcriptional program in human epidermal stem cells.
Quantifying Uncertainty and Robustness in a Biomathematical Model Based Patient-Specific Response Metric for Glioblastoma
Authors: Hawkins-Daarud Andrea , Johnston Sandra K. , Swanson Kristin R. 
Published: May 2018

AbstractGlioblastomas, lethal primary brain tumors, are known for their heterogeneity and invasiveness. A growing literature has been developed demonstrating the clinical relevance of a biomathematical model, the Proliferation-Invasion (PI) model, of glioblastoma growth. Of interest here is the development of a treatment response metric, Days Gained (DG). This metric is based on individual tumor kinetics estimated through segmented volumes of hyperintense regions on T1-weighted gadolinium enhanced (T1Gd) and T2-weighted magnetic resonance images (MRIs). This metric was shown to be prognostic of time to progression. Further, it was shown to be more prognostic of outcome than standard response metrics. While promising, the original paper did not account for uncertainty in the calculation of the DG metric leaving the robustness of this cutoff in question. We harness the Bayesian framework to consider the impact of two sources of uncertainty: 1) image acquisition and 2) interobserver error in image segmentation. We first utilize synthetic data to characterize what non-error variants are influencing the final uncertainty in the DG metric. We then consider the original patient cohort to investigate clinical patterns of uncertainty and to determine how robust this metric is for predicting time to progression and overall survival. Our results indicate that the key clinical variants are the time between pre-treatment images and the underlying tumor growth kinetics, matching our observations in the clinical cohort. Finally, we demonstrated that for this cohort there was a continuous range of cutoffs between 94 and 105 for which the prediction of the time to progression and was over 80% reliable. While further validation must be done, this work represents a key step in ascertaining the clinical utility of this metric.
Annelid brain and nerve cord in siboglinidRiftia pachyptila
Authors: Rimskaya-Korsakova Nadezhda N. , Galkin Sergey V. , Malakhov Vladimir V. 
Published: May 2018

AbstractVestimentifera is a peculiar group of marine gutless siboglinids which has uncertain position in annelid tree. The detailed study of the fragmentary explored central nervous system of vestimentiferans and other siboglinids is requested to trace the evolution of the siboglinid group. Among all siboglinids the vestimentiferans preserve the gut rudiment what makes them a key group to homologize main cerebral structures with the ones of typical annelids, such as supra- and subesophageal commissures, cirsumesophageal connectives etc. Histologically we revealed main annelid brain structures in the compact large brain ofRiftia pachyptila: circumesophageal connectives (longitudinal nerve tracts) and commissures (dorsal, supra- and subenteral commissures). Innervation of tentacles makes them homologous to peristomial palps of the rest annelids. The single nerve cord is represented by paired intraepidermal longitudinal strands associated with the ventral ciliary field in vestimentum and bearing giant axons originating from at least four pairs of perikarya. The absence of regularly positioned ganglia and lateral nerves in the nerve cord in vestimentum and trunk and presence of them in the opisthosome segments. Among siboglinids, the vestimentiferans distinguished by a large and significatly differentiated brain which is reflection of the high development of the palp apparatus.Osedax, frenulates andSclerolinumhave less developped brain. Frenulates andSclerolinumhave good ganglionization in the opisthosome, which probably indicates its high mobility. Comparative neuroanatomical analysis of the siboglinids and annelid sister clades allows us to hypothesize that the last common ancestor of siboglinids might had brain with a dorsal commissure giving rise neurite bundles to palps and paired ventral nerve cord.
Acquisition premiums and the recognition of identifiable intangible assets in business combinations pre- and post-IFRS adoption
Authors: Su Wun Hong , Wells Peter 
Published: May 2018

PurposeThis paper aims to evaluate the relation between acquisition premiums and amounts recognised as identifiable intangible assets (IIAs) in business combination, in periods before and after transition to International Financial Reporting Standards (IFRS).Design/methodology/approachThis is an empirical archival research using data from business acquisitions.FindingsIn the pre-IFRS period, there is evidence of firms recognising IIAs in business combinations having higher acquisition premiums. This association of acquisition premiums and IIAs ceased with transition to IFRS, notwithstanding the relative latitude provided in accounting standards for the recognition of IIAs.Research limitations/implicationsThis paper complements the study by Su and Wells (2015) which founds little association between IIAs and performance subsequent to business acquisitions prior to transition to IFRS. The results here suggest that it is attributable to overpayment. Problematically, the incentives for opportunism remain and an issue requiring address is whether alternative sources of accounting flexibility in relation to business combinations exist, such as goodwill which is no longer subject to mandatory amortisation.Practical implicationsThe results are consistent with accounting opportunism and suggest “overpayment” and accounting flexibility having an economic consequence. This would be expected to result in asset impairments in subsequent periods; however, there is little evidence of this occurring.Social implicationsThese results have relevance for regulators concerned with the operation of regulation relating to business acquisitions (AASB 3) and intangible assets (AASB 138).Originality/valueThis paper complements a number of papers concerned with the recognition of IIAs in business combinations and confirms what many researchers in the area typically assume (triangulation).
Attaining elite leadership: career development and childhood socioeconomic status
Authors: Jones-Morales Jennifer , Konrad Alison M. 
Published: May 2018

PurposeThe existence of disadvantaged sub-populations whose talents are under-leveraged is a problem faced by developing and developed countries alike. Life history data revealed that a large proportion of elite business leaders in the Caribbean emerged from childhood poverty (families subsisting on US$1-2 a day, 40 percent). The purpose of this paper is to examine the key factors supporting the career development of elite leaders from a broad socioeconomic spectrum and both genders in order to build a model of career development for elite leadership.Design/methodology/approachData were collected via in-depth interviews from a deliberately gender-balanced sample of 39 male and 39 female elite business leaders. Thematic analysis identified consistencies across independent interviews and resulted in a model identifying factors supporting pre-career development as key to eventual attainment of elite leadership.FindingsFindings indicated that in childhood and youth, proactivity plus talent recognition and mentoring by adults enhanced access to early developmental opportunities. Early career mentoring guided talented youth to build personal drive, self-esteem, altruism, and integrity, which created a foundation for developing career capital through values-based action. Altogether, these findings indicate the importance of pre-career relational capital to attainment of elite career success.Originality/valueDifficult-to-access elite leaders provided rich information emphasizing the importance of pre-career development in childhood and youth to eventual elite leadership attainment. Virtually all of the elites in the sample remember being identified as talented early in life and consider early messages about drive to achieve as well as support received from parents, teachers, and other interested adults to be critical to their success. Hence, a process of talent recognition and encouragement to excel appear to be crucial for connecting young people to important relational capital allowing them to eventually achieve elite status, particularly those individuals hailing from disadvantaged backgrounds.