bluuebunny/crossref_metadata_2025_split huggingface dataset:
DAIRYdb: A manually curated gold standard reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
Authors: Meola Marco , Rifa Etienne , Shani Noam , Delbès Céline , Berthoud Hélène , Chassard Christophe 
Published: August 2018

Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. However, the close phylogenetic relationship between species encountered in dairy products requires accurate species annotation to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Taxonomy annotation in universal 16S databases with environmental sequences like Silva, RDP or Greengenes is based on predictions rather than on studies of type strains or isolates. We provide a manually curated database composed of 10’290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically.The manually curated DAIRYdb strongly improves taxonomic classification accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.
The endosomal sorting adaptor HD-PTP is required for ephrin-B:EphB signalling in cell collapse and motor axon guidance
Authors: Lahaie Sylvie , Morales Daniel , Bagci Halil , Hamoud Noumeira , Castonguay Charles-Etienne , Kazan Jalal M. , Desrochers Guillaume , Klar Avihu , Gingras Anne-Claude , Pause Arnim , Côté Jean-François , Kania Artur 
Published: August 2018

AbstractThe signalling output of many transmembrane receptors that mediate cell-cell communication is restricted by the endosomal sorting complex required for transport (ESCRT), but the impact of this machinery on Eph tyrosine kinase receptor function is unknown. We identified the ESCRT-associated adaptor protein HD-PTP as part of an EphB2 BioID interactome, and confirmed this association using co-immunoprecipitation. Although HD-PTP loss does not change EphB2 expression, it attenuates the ephrin-B2:EphB2 signalling-induced collapse of cultured cells and axonal growth cones, and results in aberrant guidance of chick spinal motor neuron axonsin vivoHD-PTP depletion abrogates ligand-induced EphB2 clustering, and EphB2 and Src family kinase activation. HD-PTP deficiency also accelerates ligand-induced EphB2 degradation, contrasting the phenotypes reported for other cell surface receptors. Our results link Eph signalling to the ESCRT machinery and demonstrate a role for HD-PTP in the earliest steps of ephrin-B:EphB signalling, as well as in obstructing premature receptor depletion.
Sostdc1 regulates natural killer cell maturation and cytotoxicity
Authors: Millan Alberto J. , Elizaldi Sonny R. , Lee Eric M. , Aceves Jeffrey O. , Murugesh Deepa , Loots Gabriela G. , Manilay Jennifer O. 
Published: August 2018

AbstractNatural killer (NK) cells are specialized lymphocytes with the innate ability to eliminate virally infected and cancerous cells, but the mechanisms that control NK cell development and cytotoxicity are incompletely understood. We identified novel roles for Sclerostin domain containing-1 (Sostdc1) in NK cell development and function.Sostdc1-knockout (Sostdc1-/-) mice display a progressive accumulation of transitional NK cells (CD27+CD11b+, tNK) with age, indicating a partial developmental block. The Ly49 repertoire on NK cells inSostdc1-/-mice is also changed. Lower frequencies ofSostdc1-/-splenic tNKs express inhibitory Ly49G2 receptors, but higher frequencies express activating Ly49H and Ly49D receptors. However, the frequencies of Ly49I+, G2+, H+and D+populations were universally decreased at the most mature (CD27-CD11b+, mNK) stage. We hypothesized that the Ly49 repertoire inSostdc1-/-mice would correlate with NK killing ability, and observed thatSostdc1-/-NK cells are hyporesponsive against MHC-I-deficient cell targetsin vitroandin vivo, despite higher CD107a surface levels and similar IFNγ expression to controls. Consistent with Sostdc1’s known role in the regulation of Wnt signaling, high levels of Wnt coactivatorsTcf7andLef1were observed inSostdc1-/-NK cells. Expression of the NK development geneId2was decreased inSostdc1-/-iNK and tNK cells, but we observed no changes inEomesandTbx21expression. Reciprocal bone marrow transplant experiments showed thatSostdc1regulates NK cell maturation and expression of Ly49 receptors in a cell-extrinsic fashion from both non-hematopoietic and hematopoietic sources. Taken together, these data support a role forSostdc1in the regulation of NK cell maturation, and NK cell cytotoxicity, and identify potential NK cell niches.Summary of ResultsSostdc1-/-mice display a partial block between the tNK and mNK developmental stages.Sostdc1influences the Ly49 receptor repertoire on NK cells.NK cells inSostdc1-/-mice display impaired ability to killβ2m-/-target cells.Sostdc1-/-NK cell subsets express high levels of Wnt coactivatorsTcf7andLef1.Id2expression is decreased in iNK and tNK cells in the absence ofSostdc1.Bone marrow transplantation experiments demonstrate cell-extrinsic regulation of NK cell maturation by Sostdc1 in both non-hematopoietic (stromal) and hematopoietic cells.
Delayed start of first-time breeding and non-breeders surplus in the Western Siberian population of the European Pied Flycatcher
Authors: Grinkov Vladimir G. , Sternberg Helmut 
Published: August 2018

ABSTRACTNon-breeders are those sexually mature individuals that do not breed in a given reproductive cycle of a population. There is a widespread belief that the presence of non-breeders can affect the actual population dynamics, as well as the population responses to environmental change (Lee et al. 2017). Sternberg (1989), using demographic data, has shown that 83% and 62% of males and females, respectively, do not breed in the first year of life in the Lower Saxony (Germany) population of the European Pied Flycatcher (Ficedula hypoleuca). Later, with experimental removal of males, it has been proven that in the Lower Saxony and Moscow Region (Russia) populations, there are many non-breeding males (Sternberg et al. 2002). For the Netherlands population of the European Pied Flycatcher, the presence of a large number of non-breeders has been demonstrated using experimental removals for both males and females (Both et al. 2017). Here we have estimated the number of non-breeders in the Western Siberian population of the European Pied Flycatcher using demographic data (11 cohorts from 2001 to 2011 of birth) and experimental removal of males. We have shown that both males and females can start to breed at the age of one to five years. The proportion of non-breeders can be 59.5% and 68.5% for first-year males and females, respectively. We discuss the differences in the proportion of non-breeders between the Western Siberian and European populations of the European Pied Flycatcher, as well as factors affecting the number of non-breeders.
Forecasting bacterial survival-success and adaptive evolution through multi-omics stress-response mapping, network analyses and machine learning
Authors: Zhu Zeyu , Surujon Defne , Pavao Aidan , Bento José , van Opijnen Tim 
Published: August 2018

ABSTRACTWhether a bacterial pathogen establishes an infection and/or evolves antibiotic resistance depends on successful survival while experiencing stress from for instance the host immune system and/or antibiotics. Predictions on bacterial survival and adaptive outcomes could thus have great prognostic value. However, it is unknown what information is required to enable such predictions. By developing a novel network-based analysis method, a bacterium's phenotypic and transcriptional response can be objectively quantified in temporal 3D-feature space. The resulting trajectories can be interpreted as a degree of coordination, where a focused and coordinated response predicts bacterial survival-success, and a random uncoordinated response predicts survival-failure. These predictions extend to both antibiotic resistance and in vivo infection conditions and are applicable to both Gram-positive and Gram-negative bacteria. Moreover, through experimental evolution we show that the degree of coordination is an adaptive outcome - an uncoordinated response evolves into a coordinated response when a bacterium adapts to its environment. Most surprisingly, it turns out that phenotypic and transcriptional response data, network features and genome plasticity data can be used to train a machine learning model that is able to predict which genes in the genome will adapt under nutrient or antibiotic selection. Importantly, this suggests that deterministic factors help drive adaptation and that evolution is, at least partially, predictable. This work demonstrates that with the right information predictions on bacterial short-term survival and long-term adaptive outcomes are feasible, which underscores that personalized infectious disease diagnostics and treatments are possible, and should be developed.
Predicting the future direction of cell movement with convolutional neural networks
Authors: Nishimoto Shori , Tokuoka Yuta , Yamada Takahiro G , Hiroi Noriko F , Funahashi Akira 
Published: August 2018

SummaryImage-based deep learning systems, such as convolutional neural networks (CNNs), have recently been applied to cell classification, producing impressive results; however, application of CNNs has been confined to classification of the current cell state from the image. Here, we focused on cell movement where current and/or past cell shape can influence the future cell fate. We demonstrate that CNNs prospectively predicted the future direction of cell movement with high accuracy from a single image patch of a cell at a certain time. Furthermore, by visualizing the image features that were learned by the CNNs, we could identify morphological features, e.g., the protrusions and trailing edge that have been experimentally reported to determine the direction of cell movement. Our results indicate that CNNs have the potential to predict the future cell fate from current cell shape, and can be used to automatically identify those morphological features that influence future cell fate.
Contrast sensitivity reveals an oculomotor strategy for temporally encoding space
Authors: Casile Antonino , Victor Jonathan , Rucci Michele 
Published: August 2018

AbstractThe contrast sensitivity function (CSF), how sensitivity varies with the spatial frequency of the stimulus, is a fundamental assessment of visual performance. The CSF is generally assumed to be determined by low-level sensory processes. However, the sensitivities of neurons in the early visual pathways, as measured in experiments with immobilized eyes, diverge from psychophysical CSF measurements in primates. Under natural viewing conditions, as in typical psychophysical measurements, humans continually move their eyes, drifting in a seemingly erratic manner even when looking at a fixed point. Here, we show that the resulting transformation of the visual scene into a spatiotemporal flow on the retina constitutes a processing stage that reconciles human CSF and the response characteristics of retinal ganglion cells under a broad range of conditions. Our findings suggest a fundamental integration between perception and action: eye movements work synergistically with the sensitivities of retinal neurons to encode spatial information.
Candidate genes under balancing selection in a plant bacterial pathogen
Authors: Castillo José A. , Agathos Spiros N. 
Published: August 2018

ABSTRACTPlant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common plant bacterial pathogen. We performed a genome-wide scan ofRalstonia solanacearum,an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Using a sliding window approach, we analyzed 57 genomes from three phylotypes ofR. solanacearumto detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, Watterson’s θ and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes that map in any of the two main replicons ofR. solanacearum.The candidate genes under balancing selection are related to primary metabolism (51.3%) or directly associated to virulence (48.7%), being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.
Transposable Element Exprssion in Tumors is Associated with Immune Infiltration and Increased Antigenicity
Authors: Kong Yu , Rose Chris , Cass Ashley A. , Darwish Martine , Lianoglou Steve , Haverty Pete M. , Tong Ann-Jay , Blanchette Craig , Mellman Ira , Bourgon Richard , Greally John , Jhunjhunwala Suchit , Albert Matthew L. , Chen-Harris Haiyin 
Published: August 2018

AbstractProfound loss of DNA methylation is a well-recognized hallmark of cancer. Given its role in silencing transposable elements (TEs), we hypothesized that extensive TE expression occurs in tumors with highly demethylated DNA. We developed REdiscoverTE, a computational method for quantifying genome-wide TE expression in RNA sequencing data. Using The Cancer Genome Atlas database, we observed increased expression of over 400 TE subfamilies, of which 262 appeared to result from a proximal loss of DNA methylation. The most recurrent TEs were among the evolutionarily youngest in the genome, predominantly expressed from intergenic loci, and associated with antiviral or DNA damage responses. Treatment of glioblastoma cells with a demethylation agent resulted in both increased TE expression and de novo presentation of TE-derived peptides on MHC class I molecules. Therapeutic reactivation of tumor-specific TEs may synergize with immunotherapy by inducing both inflammation and the display of potentially immunogenic neoantigens.One Sentence SummaryTransposable element expression in tumors is associated with increased immune response and provides tumor-associated antigens
A speech envelope landmark for syllable encoding in human superior temporal gyrus
Authors: Oganian Yulia , Chang Edward F. 
Published: August 2018

AbstractListeners use the slow amplitude modulations of speech, known as the envelope, to segment continuous speech into syllables. However, the underlying neural computations are heavily debated. We used high-density intracranial cortical recordings while participants listened to natural and synthesized control speech stimuli to determine how the envelope is represented in the human superior temporal gyrus (STG), a critical auditory brain area for speech processing. We found that the STG does not encode the instantaneous, moment-by-moment amplitude envelope of speech. Rather, a zone of the middle STG detects discrete acoustic onset edges, defined by local maxima in the rate-of-change of the envelope. Acoustic analysis demonstrated that acoustic onset edges reliably cue the information-rich transition between the consonant-onset and vowel-nucleus of syllables. Furthermore, the steepness of the acoustic edge cued whether a syllable was stressed. Synthesized amplitude-modulated tone stimuli showed that steeper edges elicited monotonically greater cortical responses, confirming the encoding of relative but not absolute amplitude. Overall, encoding of the timing and magnitude of acoustic onset edges in STG underlies our perception of the syllabic rhythm of speech.
Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer
Authors: Trigos Anna S. , Pearson Richard B. , Papenfuss Anthony T. , Goode David L. 
Published: August 2018

AbstractExtensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumours, we show many transcriptional changes in tumours are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach.
Flexibly-oriented double Cdc45-MCM-GINS intermediates during eukaryotic replicative helicase maturation
Authors: Liu Lu , Zhang Yue , Zhang Jingjing , Wang Jian-Hua , Cao Qinhong , Li Zhen , Campbell Judith L. , Dong Meng-Qiu , Lou Huiqiang 
Published: August 2018

AbstractThe core of the eukaryotic helicase MCM is loaded as an inactive double hexamer (DH). How it is assembled into two active Cdc45-MCM-GINS (CMG) helicases remains elusive. Here, we report that at the onset of S phase, both Cdc45 and GINS are loaded as dimers onto MCM DH, resulting in formation of double CMG (d-CMG). As S phase proceeds, d-CMGs gradually mature into two single CMG-centered replisome progression complexes (RPCs). Mass spectra reveal that RPA and DNA Pol α/primase co-purify exclusively with RPCs, but not with d-CMGs. Consistently, d-CMGs are not able to catalyze either the unwinding or de novo DNA synthesis, while RPCs can do both. Using single-particle electron microscopy, we have obtained 2D class averages of d-CMGs. Compared to MCM DHs, they display heterogeneous, flexibly orientated and partially loosened conformations with changed interfaces. The dumbbell-shaped d-CMGs are mediated by Ctf4, while other types of d-CMGs are independent of Ctf4. These data suggest CMG dimers as bona fide intermediates during MCM maturation, providing an additional quality control for symmetric origin activation and bidirectional replication.
High-throughput characterisation of bull semen motility using differential dynamic microscopy
Authors: Jepson Alys , Arlt Jochen , Statham Jonathan , Spilman Mark , Burton Katie , Wood Tiffany , Poon Wilson C. K. , Martinez Vincent A. 
Published: August 2018

AbstractWe report a high-throughput technique for characterising the motility of spermatozoa using differential dynamic microscopy. A large field of view movie (~ 10mm2) records thousands of cells (e.g. ≈ 5000 cells even at a low cell density of 20 × 106cells/ml) at once and yields averaged measurements of the mean (υ) and standard deviation (σ) of the swimming speed, a head oscillation amplitude (A0) and frequency (f0), and the fraction of motile spermatozoa (α). Interestingly, the measurement ofαrelies on the swimming spermatozoa enhancing the motion of the non-swimming population. We demonstrate the ease and rapidity of our method by performing on-farm characterisation of bull spermatozoa motility, and validate the technique by comparing laboratory measurements with tracking. Our results confirm the long-standing theoretical prediction thatfor swimming spermatozoa.
Contractual challenges for BIM-based construction projects: a systematic review
Authors: Abd Jamil Ahmad Huzaimi , Fathi Mohamad Syazli 
Published: August 2018

Purpose
Building information modeling (BIM) has been proven to enable outstanding results in construction processes by enhancing knowledge sharing with regard to a building or facility throughout its life cycle from the conceptual design to facility management. The purpose of this paper is to investigate the extent to which the use of BIM has impacted the legal and contractual implications of the existing construction contracts for aligning the three sets of relevant development domains: BIM functionality, contract procurement methods, and BIM legal and contractual issues to enhance the efficient use of valuable resources.

Design/methodology/approach
This exploratory study was undertaken by analyzing the literature using a novel approach involving a matrix that juxtaposes BIM functionalities for each project life cycle with contract procurement methods. As part of the study, 28 interactions of BIM legal and contractual issues have been identified, as representing positive and negative interactions.

Findings
The interaction matrix framework that juxtaposes BIM functionalities and procurement methods highlights the theoretical and practical relationships identified between the methods. It also simultaneously recognizes the constructive and destructive interactions between these development domains by means of critically identifying the possible interactions of the legal and contractual aspects of both the BIM project procurement and the practical aspects of BIM project delivery.

Originality/value
The present study contributes to the existing literature by extensively identifying the probable interactions of contractual issues within BIM functionality with contract procurement methods throughout the life cycle of a building construction project.