bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal Hernia After Laparoscopic Total Gastrectomy for Gastric Cancer
Authors: Ojima Toshiyasu , Nakamori Mikihito , Nakamura Masaki , Katsuda Masahiro , Hayata Keiji , Kato Tomoya , Tsuji Toshiaki , Yamaue Hiroki 
Published: September 2017

Purpose:
The aim of this study was to clarify internal hernia (IH) characteristics after laparoscopic gastrectomy.

Materials and Methods:
This was a retrospective study of 1943 consecutive gastric cancer patients who underwent surgery at our institute between 2004 and 2015. Since 2013, our technique includes antecolic Roux-en-Y (RY) with closure of all mesenteric defects during laparoscopic total gastrectomy (LTG) as standard.

Results:
Postoperative IH was only detected in patients who underwent total gastrectomy with RY reconstruction. Furthermore, the incidence of IH was significantly higher after LTG than after open total gastrectomy (4.9% vs. 1.0%; P=0.005). IH after LTG occurred in 8.0% of patients before standardization with closure of the mesenteric defects, but no IH was observed after standardization (P=0.047).

Conclusions:
Closure of all mesenteric defects is recommended for gastric cancer patients who undergo LTG with antecolic RY. Registration number: UMIN000009163/000025029 (www.umin.ac.jp/ctr/)
Actin assembly-inducing protein ActA promotes FcγRIa-mediatedListeriainternalization
Authors: Perelman Sofya S. , Abrams Michael E. , Alto Neal M. 
Published: September 2017

AbstractListeria monocytogenesis a Gram-positive intracellular pathogen and the causative agent of human listeriosis. While the ability ofL. monocytogenesto enter and survive in professional phagocytes is critical to establish a successful infection, mechanisms of invasion are poorly understood. Our previous investigation into the role of type I interferon-stimulated genes in bacterial infection revealed that the human immunoglobulin receptor FcγRIa served as aL. monocytogenesinvasion factor. FcγRIa-mediatedL. monocytogenesentry occurred independently of immunoglobulin interaction or bacterial internalins. However, the bacterial determinants that mediate FcγRIa interaction remain unclear. Using a comparative genomics approach, we identify actin assembly-inducing protein ActA as a pathogen specific ligand of FcγRIa. FcγRIa enhanced entry of pathogenicL. monocytogenesandL. ivanoviistrain but not non-pathogenicL. innocua. We found that the major virulence regulator PrfA is required for pathogen entry into FcγRIa-expressing cells and identify its gene targetactAas the criticalListerialigand. ActA alone was sufficient to promote entry into FcγRIa-expressing cells, and this function is independent of its actin nucleating activity. Together, these studies present an unexpected role of ActA beyond its canonical function in actin-based motility and expand our understanding ofListeriastrategies for host cell invasion.ImportanceListeria monocytogenesis a food-borne bacterial pathogen and a causative agent of listeriosis with up to 50% mortality rate in immunocompromised individuals. While the mechanisms ofListeriaentry into non-phagocytic cells have been extensively characterized, the details of phagocytic cell invasion are still poorly understood. We have recently discovered that human immunoglobulin receptor FcγRIa mediatesListeriauptake by monocytic cells. This process occurred independently of canonical immunoglobulin interactions as well as classicListeriainternalization factors. Importantly, molecular determinants ofListeria-FcγRIa interaction leading to bacterial entry, remained unknown. In this study, we demonstrate thatListeriavirulence factor actin-assembly inducing protein ActA is required for FcγRIa-mediated entry. Further, ActA was found to be sufficient for the internalization, suggesting its role as a bacterial ligand of FcγRIa. Together, these findings expand our knowledge of mechanisms thatListeriahas evolved to exploit cellular signaling pathways and immune defense of the host.
The Gram-positive model organismBacillus subtilisdoes not form microscopically detectable cardiolipin-specific lipid domains
Authors: Pogmore Alex-Rose , Seistrup Kenneth H. , Strahl Henrik 
Published: September 2017

AbstractRather than being a homogenous diffusion-dominated structure, biological membranes can exhibit areas with distinct composition and characteristics commonly termed as lipid domains. Arguably the most comprehensively studied examples in bacteria are domains formed by cardiolipin, which have been functionally linked to protein targeting, cell division process, and mode of action of membrane targeting antimicrobials. Cardiolipin domains were originally identified in the Gram-negative model organismEscherichia colibased on preferential staining by the fluorescent membrane dye nonyl acridine orange (NAO), and later reported to exist also in other Gram-negative and -positive bacteria. Recently, the lipid-specificity of NAO has been questioned based on studies conducted inE. coli. This prompted us to re-analyse cardiolipin domains also in the Gram-positive model organismBacillus subtilis. Here we show that logarithmically growingB. subtilisdoes not form microscopically detectable cardiolipin-specific lipid domains, and that NAO is not a specific stain for cardiolipin in this organism.AbbreviationsNAO10-nonyl acridine orange bromideNile Red9-diethylamino-5-benzo[±]phenoxazinone
Stochastic Resonance Mediates the State-Dependent Effect of Periodic Stimulation on Cortical Alpha Oscillations
Authors: Lefebvre Jérémie , Frohlich Flavio , Hutt Axel 
Published: September 2017

ABSTRACTBrain stimulation can be used to engage and modulate rhythmic activity in cortical networks. However, the outcomes have been shown to be impacted by behavioral states and endogenous brain fluctuations. To better understand how this intrinsic oscillatory activity controls the brain’s susceptibility to stimulation, we analyzed a computational model of the thalamocortical system in both the rest and task states, to identify the mechanisms by which endogenous alpha oscillations (8Hz-12Hz) are impacted by periodic stimulation. Our analysis shows that the differences between different brain states can be explained by a passage through a bifurcation combined to stochastic resonance - a mechanism whereby irregular fluctuations amplify the response of a nonlinear system to weak signals. Indeed, our findings suggest that modulating brain oscillations is best achieved in states of low endogenous rhythmic activity, and that irregular state-dependent fluctuations in thalamic inputs shape the susceptibility of cortical population to periodic stimulation.
Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results
Authors: Alterovitz Gil , Dean Dennis , Goble Carole , Crusoe Michael R. , Soiland-Reyes Stian , Bell Amanda , Hayes Anais , Suresh Anita , Purkayastha Anjan , King Charles H. , Taylor Dan , Johanson Elaine , Thompson Elaine E. , Donaldson Eric , Morizono Hiroki , Tsang Hsinyi , Vora Jeet K. , Goecks Jeremy , Yao Jianchao , Almeida Jonas S. , Keeney Jonathon , Addepalli KanakaDurga , Krampis Konstantinos , Smith Krista M. , Guo Lydia , Walderhaug Mark , Schito Marco , Ezewudo Matthew , Guimera Nuria , Walsh Paul , Kahsay Robel , Gottipati Srikanth , Rodwell Timothy C , Bloom Toby , Lai Yuching , Simonyan Vahan , Mazumder Raja 
Published: September 2017

AbstractA personalized approach based on a patient’s or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to FAIR guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet lab procedures to computational methods. The BioCompute framework (https://osf.io/zm97b/) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCO) offer that standard, and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development”. By communication of high-throughput sequencing studies using a BCO, regulatory agencies (e.g., FDA), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next generation sequencing workflow exchange, reporting, and regulatory reviews.
The kinases PIG-1 and PAR-1 act in redundant pathways to regulate asymmetric division in the EMS blastomere ofC. elegans
Authors: Liro Malgorzata J. , Morton Diane G. , Rose Lesilee S. 
Published: September 2017

AbstractThe PAR-1 kinase ofC. elegansis localized to the posterior of the one-cell embryo and its mutations affect asymmetric spindle placement and partitioning of cytoplasmic components in the first cell cycle. However, unlike mutations in the posteriorly localized PAR-2 protein,par-1mutations do not cause failure to restrict the anterior PAR polarity complex. Further, it has been difficult to examine the role of PAR-1 in subsequent divisions due to the early defects inpar-1mutant embryos. Here we show that the PIG-1 kinase acts redundantly with PAR-1 to restrict the anterior PAR-3 protein for polarity maintenance in the one-cell embryo. By using a weak allele ofpar-1that exhibits enhanced lethality when combined with apig-1mutation we have further explored roles for these genes in subsequent divisions. We find that both PIG-1 and PAR-1 regulate spindle orientation in the EMS blastomere of the four-cell stage embryo to ensure that it undergoes an asymmetric division. In this cell, PIG-1 and PAR-1 act in parallel pathways for spindle positioning, PIG-1 in the MES-1/SRC-1 pathway and PAR-1 in the Wnt pathway.
Changes in alpha activity reveal that social opinion modulates attention allocation during face processing
Authors: Heyselaar Evelien , Mazaheri Ali , Hagoort Peter , Segaert Katrien 
Published: September 2017

AbstractParticipants’ performance differs when conducting a task in the presence of a secondary individual, moreover the opinion the participant has of this individual also plays a role. Using EEG, we investigated how previous interactions with, and evaluations of, an avatar in virtual reality subsequently influenced attentional allocation to the face of that avatar. We focused on changes in the alpha activity as an index of attentional allocation. We found that the onset of an avatar’s face whom the participant had developed a rapport with induced greater alpha suppression. This suggests greater attentional resources allocated to the interacted-with avatars. The evaluative ratings of the avatar induced a U-shaped change in alpha suppression, such that participants paid most attention when the avatar was rated as average. These results suggest that attentional allocation is thus an important element of how behaviour is altered in the presence of a secondary individual.
Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): an algorithm for MHz localization rates using standard CPUs
Authors: Martens Koen J.A. , Bader Arjen N. , Baas Sander , Rieger Bernd , Hohlbein Johannes 
Published: September 2017

AbstractWe present a fast and model-free 2D and 3D single-molecule localization algorithm that allows more than 3 million localizations per second on a standard multi-core CPU with localization accuracies in line with the most accurate algorithms currently available. Our algorithm converts the region of interest around a point spread function (PSF) to two phase vectors (phasors) by calculating the first Fourier coefficients in both x- and y-direction. The angles of these phasors are used to localize the center of the single fluorescent emitter, and the ratio of the magnitudes of the two phasors is a measure for astigmatism, which can be used to obtain depth information (z-direction). Our approach can be used both as a stand-alone algorithm for maximizing localization speed and as a first estimator for more time consuming iterative algorithms.
Long-lived rodents reveal signatures of positive selection in genes associated with lifespan and eusociality
Authors: Sahm Arne , Bens Martin , Szafranski Karol , Holtze Susanne , Groth Marco , Görlach Matthias , Calkhoven Cornelis , Müller Christine , Schwab Matthias , Kestler Hans A. , Cellerino Alessandro , Burda Hynek , Hildebrandt Thomas , Dammann Philip , Platzer Matthias 
Published: September 2017

AbstractThe genetic mechanisms that determine lifespan are poorly understood. Most research has been done on short lived animals and it is unclear if these insights can be transferred to long-lived mammals like humans. Some African mole-rats (Bathyergidae) have life expectancies that are multiple times higher than similar sized and phylogenetically closely related rodents. We obtained genomic and transcriptomic data from 17 rodent species and systematically scanned eleven lineages associated with the evolution of longevity and eusociality for positively selected genes (PSGs). The set of 319 PSGs contains regulators of mTOR and is enriched in functional terms associated with (i) processes that are regulated by the mTOR pathway, e.g. translation, autophagy and mitochondrial biogenesis, (ii) the immune system and (iii) antioxidant defense. Analyzing gene expression of PSGs during aging in the long-lived naked mole-rat and up-regulation in the short-lived rat, we found a pattern fitting the antagonistic pleiotropy theory of aging.
gene2drug: a Computational Tool for Pathway-based Rational Drug Repositioning
Authors: Napolitano Francesco , Carrella Diego , Mandriani Barbara , Pisonero Sandra , Sirci Francesco , Medina Diego , Brunetti-Pierri Nicola , Bernardo Diego di 
Published: September 2017

AbstractMotivationDrug repositioning has been proposed as an effective shortcut to drug discovery. The availability of large collections of transcriptional responses to drugs enables computational approaches to drug repositioning directly based on measured molecular effects.ResultsWe introduce a novel computational methodology for rational drug repositioning, which exploits the transcriptional responses following treatment with small molecule. Specifically, given a therapeutic target gene, a prioritisation of potential effective drugs is obtained by assessing their impact on the transcription of genes in the pathway(s) including the target. We performed in silico validation and comparison with a state-of-art technique based on similar principles. We next performed experimental validation in two different real-case drug repositioning scenarios: (i) upregulation of the glutamate-pyruvate transaminase, which has been shown to induce reduction of oxalate levels in a mouse model of primary hyperoxaluria, and (ii) activation of the transcription factor TFEB, a master regulator of lysosomal biogenesis and autophagy, whose modulation may be beneficial in neurodegenerative disorders.Availabilityfree athttp://gene2drug.tigem.itContactdibernardo@tigem.it
DNAJB1-PRKACAfusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma
Authors: Kastenhuber Edward R. , Lalazar Gadi , Houlihan Shauna L. , Tschaharganeh Darjus F. , Baslan Timour , Chen Chi-Chao , Requena David , Tian Sha , Bosbach Benedikt , Wilkinson John E. , Simon Sanford M. , Lowe Scott W. 
Published: September 2017

AbstractA segmental deletion resulting inDNAJB1-PRKACAgene fusion is now recognized as the signature genetic event of fibrolamellar hepatocellular carcinoma (FL-HCC), a rare but lethal liver cancer that primarily affects adolescents and young adults. Here, we implement CRISPR/Cas9 genome editing and transposon-mediated somatic gene transfer to demonstrate that expression of both the endogenous fusion protein or a chimeric cDNA leads to the formation of indolent liver tumors in mice that closely resemble human FL-HCC. Notably, overexpression of the wild type PRKACA was unable to fully recapitulate the oncogenic activity ofDNAJB1-PRKACA, implying that FL-HCC does not simply result from enhanced PRKACA expression. Tumorigenesis was significantly enhanced by genetic activation of β-catenin, an observation supported by evidence of recurrent Wnt pathway mutations in human FL-HCC, as well as treatment with hepatotoxin 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC), which causes tissue injury, inflammation and fibrosis. Our study validates theDNAJB1-PRKACAfusion kinase as an oncogenic driver and candidate drug target for FL-HCC and establishes a practical model for preclinical studies to identify strategies to treat this disease.SignificanceEfforts to understand and treat FL-HCC have been confounded by a lack of models that accurately reflect the genetics and biology of the disease. Here, we demonstrate that theDnajb1-Prkacagene fusion drives tumorigenesis in mice, and that fusion to DNAJB1 drives FL-HCC initiation more effectively than wild type PRKACA overexpression. The requirement of the PRKACA kinase domain in tumor initiation establishes the potential utility of kinase inhibitors targeting the fusion. By identifying genetic and environmental factors that can enhance the consistency and aggressiveness of disease progression, we reveal biological characteristics of the disease and advance a robust platform for future pre-clinical studies.
Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae
Authors: Thomson Ashley M. , Vargas Oscar M. , Dick Christopher W. 
Published: September 2017

AbstractPremise of the study: The tropical tree family Lecythidaceae has enormous ecological and economic importance in the Amazon basin. Lecythidaceae species can be difficult to identify without molecular data, however, and phylogenetic relationships within and among the most diverse genera are poorly resolved.Methods: To develop informative genetic markers for Lecythidaceae, we used genome skimming to assemble de novo the full plastome of the Brazil nut tree (Bertholletia excelsa) and 23 other Lecythidaceae species. Indices of nucleotide diversity and phylogenetic signal were used to identify regions suitable for genetic marker development.Results: The B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure. Using the 24 plastome alignments, we developed primers for 10 coding and non-coding DNA regions containing exceptional nucleotide diversity and phylogenetic signal. We additionally developed 19 chloroplast simple sequence repeats (cpSSRs) for population-level studies.Discussion: The coding region ycf1 and the spacer rpl16-rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic. The plastomes and primers presented in this study will facilitate a broad array of ecological and evolutionary studies in Lecythidaceae.
A pan-cancer landscape of interactions between solid tumors and infiltrating immune cell populations
Authors: Tamborero David , Rubio-Perez Carlota , Muiños Ferran , Radhakrishnan Sabarinathan , Piulats Josep M , Muntasell Aura , Dienstmann Rodrigo , Lopez-Bigas Nuria , Gonzalez-Perez Abel 
Published: September 2017

ABSTRACTThroughout their development, tumors are challenged by the immune system and acquire features to evade its surveillance. A systematic view of these traits is still lacking. Here, we identify genomic and transcriptomic traits associated to the immune-phenotype of 9,403 tumors of 29 solid cancers. In highly cytotoxic immune-phenotypes we found tumors with low clonal heterogeneity enriched by alterations of genes involved in epigenetic regulation, ubiquitin mediated proteolysis, antigen-presentation and cell-cell communication, which may drive resistance. Tumors with immune-phenotypes with mid cytotoxicity present an over-activation of processes involved in invasion and remodeling of neighboring tissues that may foster the recruitment of immune-suppressive cells. Tumors with poor cytotoxic immune-phenotype tend to be of more advanced stages and present frequent alterations in cell cycle, hedgehog, beta-catenin and TGF-beta pathways, which may drive the immune depletion. These results may be exploited to develop novel combinatorial targeting strategies involving immunotherapies.
A random-dot kinematogram for web-based vision research
Authors: Rajananda Sivananda , Lau Hakwan , Odegaard Brian 
Published: September 2017

AbstractWeb-­based experiments using visual stimuli have become increasingly common in recent years, but many frequently-used stimuli in vision research have yet to be developed for online platforms. Here, we introduce the first open access random-dot kinematogram (RDK) for use in web browsers. This fully customizable RDK offers options to implement several different types of noise (random position, random walk, random direction) and parameters to control aperture shape, coherence level, the number of dots, and other features. We include links to commented JavaScript code for easy implementation in web-based experiments, as well as an example of how this stimulus can be integrated as a plugin with a JavaScript library for online studies (jsPsych).