bluuebunny/crossref_metadata_2025_split huggingface dataset:
ENSO Drives interannual variation of forest woody growth across the tropics
Authors: Rifai Sami W. , Girardin Cécile A. J. , Berenguer Erika , del Aguila-Pasquel Jhon , Dahlsjö Cecilia A. L. , Doughty Christopher E. , Jeffery Kathryn J. , Moore Sam , Oliveras Imma , Riutta Terhi , Rowland Lucy M. , Murakami Alejandro Araujo , Addo-Danso Shalom D. , Brando Paulo , Burton Chad , Ondo Fidèle Evouna , Duah-Gyamfi Akwasi , Amézquita Filio Farfán , Freitag Renata , Pacha Fernando Hancco , Huasco Walter Huaraca , Ibrahim Forzia , Mbou Armel T. , Mihindou Vianet Mihindou , Peixoto Karine S. , Rocha Wanderley , Rossi Liana C. , Seixas Marina , Silva-Espejo Javier E. , Abernethy Katharine A. , Adu-Bredu Stephen , Barlow Jos , da Costa Antonio C. L. , Marimon Beatriz S. , Marimon-Junior Ben H. , Meir Patrick , Metcalfe Daniel B. , Phillips Oliver L. , White Lee J. T. , Malhi Yadvinder 
Published: October 2018

Meteorological extreme events such as El Niño events are expected to affect tropical forest net primary production (NPP) and woody growth, but there has been no large-scale empirical validation of this expectation. We collected a large high–temporal resolution dataset (for 1–13 years depending upon location) of more than 172 000 stem growth measurements using dendrometer bands from across 14 regions spanning Amazonia, Africa and Borneo in order to test how much month-to-month variation in stand-level woody growth of adult tree stems (NPPstem) can be explained by seasonal variation and interannual meteorological anomalies. A key finding is that woody growth responds differently to meteorological variation between tropical forests with a dry season (where monthly rainfall is less than 100 mm), and aseasonal wet forests lacking a consistent dry season. In seasonal tropical forests, a high degree of variation in woody growth can be predicted from seasonal variation in temperature, vapour pressure deficit, in addition to anomalies of soil water deficit and shortwave radiation. The variation of aseasonal wet forest woody growth is best predicted by the anomalies of vapour pressure deficit, water deficit and shortwave radiation. In total, we predict the total live woody production of the global tropical forest biome to be 2.16 Pg C yr−1, with an interannual range 1.96–2.26 Pg C yr−1between 1996–2016, and with the sharpest declines during the strong El Niño events of 1997/8 and 2015/6. There is high geographical variation in hotspots of El Niño–associated impacts, with weak impacts in Africa, and strongly negative impacts in parts of Southeast Asia and extensive regions across central and eastern Amazonia. Overall, there is high correlation (r= −0.75) between the annual anomaly of tropical forest woody growth and the annual mean of the El Niño 3.4 index, driven mainly by strong correlations with anomalies of soil water deficit, vapour pressure deficit and shortwave radiation.This article is part of the discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
Aquaporin-4 facilitator TGN-073 demonstrates novel analgesic activity
Authors: Huber Vincent J. , Kwee Ingrid L. , Nakada Tsutomu 
Published: October 2018

AbstractDuring pre-clinical development, we tested the novel, internally developed AQP-4 facilitator TGN-073 for its effect in a rodent pain model. Therein, TGN-073 was found to exert a strong analgesic effect. Following a single 200 mg/kg (i.p.) administration of TGN-073, a virtually complete block in the acetic acid writhing test was observed. Subsequent in vitro tests demonstrated that TGN-073 had no binding affinity for the μ-opioid or NK-1 receptors. Accordingly, we suspect TGN-073 or other AQP-4 facilitators may be developed into potent non-opioid analgesic agents. Given the potential significance of this discovery, we feel it should be openly shared with the scientific community.
The perils of interaction prediction
Authors: Mao Weiguang , Kostka Dennis , Chikina Maria 
Published: October 2018

AbstractThe availability of genome-wide maps of enhancer-promoter interactions (EPIs) has made it possible to use machine learning approaches to extract and interpret features that determine these interactions in different biological contexts. Multiple methods have claimed to accomplish the task of predicting enhancer-promoter interactions based on corresponding genomic features, but this problem is actually still far from being solved. In our analysis, we show that individual enhancer and promoter regions have widely different marginal interaction probabilities, e.g. propensities, which can lead to overfitting and memorization when random cross-validation is employed. Further even when a proper cross-validation scheme is adopted, a simple propensity-based model can still achieve a competitive performance without capturing any information about the EPI mechanism.
G-quadruplex formation on specific surface-exposed regions of the human ribosomal RNA
Authors: Mestre-Fos Santi , Penev Petar I. , Suttapitugsakul Suttipong , Ito Chieri , Petrov Anton S. , Wartell Roger M. , Wu Ronghu , Williams Loren Dean 
Published: October 2018

ABSTRACTProfound similarities and critical differences mark ribosomes across phylogeny. The ribosomal core, approximated by the prokaryotic ribosome, is universal, yet mammalian ribosomes are nearly twice as large as those of prokaryotes. Differences in size are due in part to rRNA expansion segments. Here we show rRNA tentacles of Expansion Segment 7 (ES7) of Homo sapiens can form G-quadruplexes in vitro. G-quadruplex-forming regions are located on the most surface-exposed regions of the ribosome, near the termini of rRNA tentacles. We characterized rRNA of the large ribosomal subunit by computation, circular dichroism, gel mobility, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts and blotting. We investigated ES7 and oligomers derived from ES7, intact 28S rRNA, and 80S ribosomes and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. Proteins that associate with rRNA G-quadruplexes include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins (hnRNPs). And finally, by multiple sequence alignments, we observed that G-quadruplex-forming sequences appear to be a general feature LSU rRNA of the phylum Chordata but not in other phyla. It is known that G-quadruplexes form in telomeres, promoters, and untranslated regions of mRNA but, to our knowledge, they have not been reported previously in ribosomes.
EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA
Authors: Gruenstaeudl Michael , Hartmaring Yannick 
Published: October 2018

AbstractBackgroundThe submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding.MethodsA Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called “checklists”) for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled “EMBL2checklists”, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA.ResultsEMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study.DiscussionEMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.
Emergence of enteroaggregativeEscherichia coliwithin the ST131 lineage as a cause of extraintestinal infections
Authors: Boll Erik J. , Stegger Marc , Hasman Henrik , Roer Louise , Overballe-Petersen Søren , Ng Kim , Scheutz Flemming , Hammerum Anette M. , Dungu Arnold , Hansen Frank , Lilje Berit , Schrøder Hansen Dennis , Krogfelt Karen A. , Price Lance B. , Johnson James R. , Struve Carsten , Olesen Bente 
Published: October 2018

AbstractEscherichia colisequence type 131 (ST131) is a major cause of urinary and bloodstream infections and its association with extended-spectrum β-lactamases (ESBL) significantly complicates treatment. Most notorious is its rapidly expandingH30-Rx clade (named for containing allele 30 of the type-1 fimbrial adhesin genefimHand extensive antimicrobial resistance), which appears to have emerged in the United States due in part due to the acquisition of the ESBL-encodingblaCTX-M-15gene and resistance to fluoroquinolones. However, non-H30 ST131 lineages with acquired CTX-M-type resistance genes also are emerging. Based on whole-genome analyses, we describe here the presence of an (fimH)H27E. coliST131 lineage that currently is causing an outbreak of community-acquired bacteremia and recurrent urinary tract infections (UTIs) in Denmark. This lineage has acquired both a virulence plasmid (pAA) that defines the enteroaggregativeE. coli(EAEC) diarrheagenic pathotype and multiple genes associated with extraintestinalE. coli(ExPEC) that combined has made this particular ST131 lineage highly successful at colonizing its human host and cause recurrent UTI. Moreover, using a historic World Health OrganizationE. colicollection and publically available genome sequences, we identify a globalH27 EAEC ST131 lineage dating back as far as 1998. MostH27 EAEC ST131 isolates harbor pAA or pAA-like plasmids, which analysis strongly imply was caused by a single ancestral acquisition. These findings illustrate the profound plasticity of this important pathogenicE. coli H27 lineage in general, and the genetic acquisitions of EAEC-specific virulence traits that likely confer an enhanced ability to cause intestinal colonization.ImportanceTheE. coliST131 lineage is a notorious extraintestinal pathogen. A signature characteristic of ST131 is its ability to asymptomatically colonize the gastrointestinal tract and then opportunistically cause extraintestinal infections, such as cystitis, pyelonephritis and urosepsis. In this study, we report a novel ST131 sublineage that has acquired the enteroaggregative diarrheagenic phenotype, spread across multiple continents and has been associated with multiple outbreaks of community-acquired bloodstream infections in Denmark. The strain’s ability to both cause diarrhea and colonize the human gastrointestinal tract may facilitate its dissemination and establishment in the community, whereas the strain’s clonal nature may facilitate targeted control strategies, such as vaccination.
Inner-membrane GspF of the bacterial type II secretion system is a dimeric adaptor mediating pseudopilus biogenesis
Authors: Van Putte Wouter , De Vos Tatjana , Van Den Broeck Wim , Stahlberg Henning , Kudryashev Misha , Savvides Savvas N. 
Published: October 2018

AbstractThe type II secretion system (T2SS), a protein complex spanning the bacterial envelope, is pivotal to bacterial pathogenicity. Central to T2SS function is the extrusion of protein cargos from the periplasm into the extracellular environment mediated by a pseudopilus and motorized by a cytosolic ATPase. GspF, an inner-membrane component of T2SS has long been considered to be a key player in this process, yet the structural basis of its role had remained elusive. Here, we employed single-particle electron microscopy based on XcpS (GspF) from the T2SS of pathogenicP. aeruginosastabilized by a nanobody, to show that XcpS adopts a dimeric structure mediated by its transmembrane helices. This assembly matches in terms of overall organization and dimensions the basal inner-membrane cassette of a T2SS machinery. Thus, GspF is poised to serve as an adaptor involved in the mediation of propeller-like torque generated by the motor ATPase to the secretion pseudopilus.Non-technical author summaryAntibiotic resistance by bacteria imposes a worldwide threat that can only be overcome through a multi-front approach: preventive actions and the parallel development of novel molecular strategies to combat antibiotic resistance mechanisms. One such strategy might focus on antivirulence drugs that prevent host invasion and spreading by pathogenic bacteria, without shutting down essential functions related to bacterial survival. The rationale behind such an approach is that it might limit selective pressure leading to slower evolutionary rates of resistant bacterial strains. Bacterial secretion systems are an appropriate target for such therapeutic approaches as their impairment will inhibit the secretion of a multitude of virulence factors. This study focuses on the structural characterization of one of the proteins residing in the inner-membrane cassette of the type II secretion system (T2SS), a multi-protein complex in multiple opportunistic pathogens that secretes virulence factors. The targeted protein is essential for the assembly of the pseudopilus, a rod-like supramolecular structure that propels the secretion of virulence factors by pathogenic Gram-negative bacteria. Our study crucially complements growing evidence supporting a rotational assembly model of the pseudopilus and contributes to a better understanding of the functioning of the T2SS and the related secretion systems. We envisage that such knowledge will facilitate targeting of these systems for therapeutic purposes.
Sleep restriction caused impaired emotional regulation without detectable brain activation changes – a functional magnetic resonance imaging study
Authors: Tamm Sandra , Nilsonne Gustav , Schwarz Johanna , Golkar Armita , Kecklund Göran , Petrovic Predrag , Fischer Håkan , Åkerstedt Torbjörn , Lekander Mats 
Published: October 2018

SummarySleep restriction has been proposed to cause impaired emotional processing and emotional regulation by inhibiting top-down control from prefrontal cortex to amygdala. Intentional emotional regulation after sleep restriction has however never been studied using brain imaging. We here aimed to investigate the effect of sleep restriction on emotional regulation through cognitive reappraisal. Forty-seven young (age 20-30) and 33 older (age 65-75) participants (38/23 with complete data and successful sleep intervention) performed a cognitive reappraisal task during fMRI after a night of normal sleep and after restricted sleep (3h). Emotional downregulation was associated with significantly increased activity in dorsolateral prefrontal cortex (pFWE < 0.05) and lateral orbital cortex (pFWE < 0.05) in young, but not in older subjects. Sleep restriction was associated with a decrease in self-reported regulation success to negative stimuli (p < 0.01) and a trend towards perceiving all stimuli as less negative (p = 0.07), in young participants. No effects of sleep restriction on brain activity nor connectivity were found in either age group. In conclusion, our data do not support the idea of a prefrontal-amygdala disconnect after sleep restriction, and neural mechanisms underlying behavioural effects on emotional regulation after insufficient sleep require further investigation.
Molecular basis for high affinity agonist binding in GPCRs
Authors: Warne Tony , Edwards Patricia C. , Doré Andrew S. , Leslie Andrew G. W. , Tate Christopher G. 
Published: October 2018

AbstractA characteristic of GPCRs in the G protein-coupled state is that the affinity of the agonist often increases significantly, but the molecular basis for this is unclear. We have determined six active-state structures of the β1-adrenoceptor (β1AR) bound to conformation-specific nanobodies in the presence of agonists of varying efficacy. A direct comparison with structures of β1AR in inactive states bound to the identical ligands showed a 24-42% reduction in the volume of the orthosteric binding site. Potential hydrogen bonds were also shorter, and there was up to a 30% increase in the number of atomic contacts between the receptor and ligand. GPCRs are highly conserved, so these factors will likely be essential in increasing the affinity of a wide range of structurally distinct agonists.One Sentence SummaryHigh affinity agonist binding to G protein-coupled GPCRs results from an increase in the number and strength of protein-ligand interactions.
Locations in the Neocortex: A Theory of Sensorimotor Object Recognition Using Cortical Grid Cells
Authors: Lewis Marcus , Purdy Scott , Ahmad Subutai , Hawkins Jeff 
Published: October 2018

ABSTRACTThe neocortex is capable of anticipating the sensory results of movement but the neural mechanisms are poorly understood. In the entorhinal cortex, grid cells represent the location of an animal in its environment, and this location is updated through movement and path integration. In this paper, we propose that sensory neocortex incorporates movement using grid cell-like neurons that represent the location of sensors on an object. We describe a two-layer neural network model that uses cortical grid cells and path integration to robustly learn and recognize objects through movement and predict sensory stimuli after movement. A layer of cells consisting of several grid cell-like modules represents a location in the reference frame of a specific object. Another layer of cells which processes sensory input receives this location input as context and uses it to encode the sensory input in the object’s reference frame. Sensory input causes the network to invoke previously learned locations that are consistent with the input, and motor input causes the network to update those locations. Simulations show that the model can learn hundreds of objects even when object features alone are insufficient for disambiguation. We discuss the relationship of the model to cortical circuitry and suggest that the reciprocal connections between layers 4 and 6 fit the requirements of the model. We propose that the subgranular layers of cortical columns employ grid cell-like mechanisms to represent object specific locations that are updated through movement.
KPNA2 promotes cellular proliferation and inhibits apoptosis in the Saos-2 osteosarcoma cell line
Authors: Wei Dinglu , Ge Qiaofeng , Sun Xiaojuan , Zhang Long , Li Jia , Chen Chenglong , Lv Zhi 
Published: October 2018

AbstractKaryopherin α2 plays a critical role in tumorigenesis and tumor progression. However, nothing is currently known about the effects of KPNA2 on osteosarcomas. This study aimed to investigate differential KPNA2 protein and mRNA expression in human osteosarcoma tumor cells and normal bone tissue. We also sought to determine whether KPNA2 can influence the proliferation and apoptosis of the Saos-2 osteosarcoma cell line. Immunohistochemistry (IHC) was used to investigate KPNA2 protein expression. Real-time quantitative PCR (qPCR) was used to detect levels of KPNA2 mRNA expression, and lentivirus-mediated short-hairpin RNAs (shRNAs) were used to knock down KPNA2 expression in Saos-2 cells. The MTT assay and multiparametric high-content screening (HCS) were used to measure cell proliferation and growth, respectively. Flow cytometry was conducted to detect cell cycle distribution and apoptosis. The results revealed significantly higher KPNA2 expression levels in osteosarcoma tissues than in normal bone tissues; furthermore, KPNA2 mRNA was also highly expressed in three osteosarcoma cell lines. After transducing Saos-2 cells with KPNA2-shRNA lentivirus, the proliferative rate was notably decreased compared to that of the negative control (NC) lentivirus group (P<0.05). Flow cytometry results indicated that KPNA2 may arrest cell cycle progression and regulate the growth of these cells. The results for apoptosis indicated an apoptotic rate of 13.38±0.48% in KPNA2-shRNA cells, which was significantly higher than the rate for cells in the control group (5.13 ±0.33%). Therefore, this study showed that KPNA2 is highly expressed in osteosarcoma tissues and that reduced KPNA2mRNA levels inhibited proliferation and promoted apoptosis in an osteosarcoma cell line.
Molecular detection of virulence and resistance genes in Salmonella enterica serovar Typhi and Paratyphi A, B and C isolated from human diarrhea samples and lettuce in Burkina Faso
Authors: Somda Namwin Siourimè , Savadogo Aly , Bonkoungou Juste Isidore Ouindgueta , Traoré Oumar , Sambe-Ba Bissoume , Wane Abdoul Aziz , Traoré Yves , Gassama-Sow Amy 
Published: October 2018

AbstractObjectivesIn Burkina Faso (BF), dirty water, in particular those of the stoppings and the gutter are used for irrigation of vegetables. The aim of this study is to contribute to the knowledge on the molecular level of Salmonella Typhi and Paratyphi circulating in the hospitals and environment next to hospitals in BF.MethodsSalmonella Typhi and Paratyphi strains isolated from patients between 2009 to 2015 and lettuce samples isolated in 2014 in BF were characterized by simple PCR using specific primers.ResultsOut of 100 Salmonella isolated, 53% were from human and 47% from lettuce samples. Globally, the highest prevalence was observed with invA, misL, pipD, orfL and spvR genes in 97%, 96%; 74%; and 21%. Forty of these isolates carried class 1 integron, 31 from clinical samples and 9 from lettuce samples. Sequencing showed seven different gene cassette arrangements, with aadA1 in 13/15 strains, aadA7 and aac(3)-Id in 2/15 strains. Eight percent (8/100) of Salmonella harbored gyrB and parE genes with 6 from clinical and 2 from lettuce isolates. Sequencing showed no mutation in these genes. Three distinct PFGE types were observed from clinical samples with 90-95% similarity in each case. All Salmonella from lettuce had similar pulsotypes.ConclusionThis study showed the diversity virulence and resistance genes harbored of S. Typhi and Paratyphi from both clinical and lettuce samples in BF. Lettuce is a potential source of transmission of Salmonella causing diarrhea among human in BF.