bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensorimotor characteristics of sign translations modulate EEG when deaf signers read English
Authors: Quandt Lorna C. , Kubicek Emily 
Published: July 2018

ABSTRACTBilingual individuals automatically translate written words from one language to another. While this process is established in spoken-language bilinguals, there is less known about its occurrence in deaf bilinguals who know signed and spoken languages. Since sign language uses motion and space to convey linguistic content, it is possible that action simulation in the brain’s sensorimotor system plays a role in this process. We recorded EEG from deaf participants fluent in ASL as they read individual English words and found significant differences in alpha and beta EEG at central electrode sites during the reading of English words whose ASL translations use two hands, compared to English words whose ASL translations use one hand. Hearing non-signers did not show any differences between conditions. These results demonstrate the involvement of the sensorimotor system in cross-linguistic, cross-modal translation, and suggest that action simulation processes may be key to deaf signers’ language concepts.
Neutrality in the Metaorganism
Authors: Sieber Michael , Pita Lucía , Weiland-Bräuer Nancy , Dirksen Philipp , Wang Jun , Mortzfeld Benedikt , Franzenburg Sören , Schmitz Ruth A. , Baines John F. , Fraune Sebastian , Hentschel Ute , Schulenburg Hinrich , Bosch Thomas C. G. , Traulsen Arne 
Published: July 2018

AbstractAlmost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and which are therefore interesting candidates for further study. Moreover, using simulated communities we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.
Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device
Authors: Treuren Will Van , Brower Kara K. , Labanieh Louai , Hunt Daniel , Lensch Sarah , Cruz Bianca , Cartwright Heather N. , Tran Cawa , Fordyce Polly M. 
Published: July 2018

AbstractCoral reefs, and their associated diverse ecosystems, are of enormous ecological importance. In recent years, coral health has been severely impacted by environmental stressors brought on by human activity and climate change, threatening the extinction of several major reef ecosystems. Reef damage is mediated by a process called ‘coral bleaching’ where corals, sea anemones, and other cnidarians lose their photosynthetic algal symbionts (genus Symbiodinium) upon stress induction, resulting in drastically decreased host energy harvest and, ultimately, coral death. The mechanism by which this critical cnidarian-algal symbiosis is lost remains poorly understood. Here, we report ‘Traptasia’, a simple microfluidic device with multiple traps designed to isolate and image individual live larvae of Aiptasia, a sea anemone model organism, and their algal symbionts over extended time courses. Aiptasia larvae are ~100 μm in length, deformable, and highly motile, posing particular challenges for long-term imaging. Using a trap design optimized via fluid flow simulations and polymer bead loading tests, we trapped Aiptasia larvae containing algal symbionts and demonstrated stable imaging for >10 hours. We visualized algal migration within Aiptasia larvae and observed algal expulsion under an environmental stressor. To our knowledge, this device is the first to enable live imaging of cnidarian larvae and their algal symbionts and, in further implementation, could provide important insights into the cellular mechanisms of coral bleaching under different environmental stressors. The device is simple to use, requires minimal external equipment and no specialized training to operate, and can easily be adapted to study a variety of large, motile organisms.
Making headlines: An analysis of US government-funded cancer research mentioned in online media
Authors: Maggio Lauren A. , Ratcliff Chelsea L. , Krakow Melinda , Moorhead Laura , Enkhbayar Asura , Alperin Juan Pablo 
Published: July 2018

AbstractBackgroundConsiderable resources are devoted to producing knowledge about cancer, which in turn is disseminated to policymakers, practitioners, and the public. Online media are a key dissemination channel for cancer research. Yet which cancer research receives media attention is not well understood. Understanding the characteristics of journal articles that receive media attention is crucial to optimize research dissemination.MethodsThis cross-sectional study examines journal articles on cancer funded by the US government published in 2016, using data from PubMed and Altmetric to determine whether an article received online media attention. Frequencies and proportions were calculated to describe the cancer types and continuum stages covered in journal articles.Results16.8% of articles published on US government-funded research were covered in the media. Published journal articles addressed all common cancers. Roughly one-fourth to one-fifth of journal articles within each cancer category received online media attention. Media mentions were disproportionate to actual burden of each cancer type (ie, incidence and mortality), with breast cancer articles receiving the most media mentions. Cancer prevention and control articles received less online media attention than diagnosis or therapy articles.ConclusionFindings revealed a mismatch between prevalent cancers and cancers highlighted in the media. Further, journal articles on cancer control and prevention received less media attention than other cancer continuum stages. Media mentions were not proportional to actual public cancer burden nor volume of scientific publications in each cancer category. Results highlight a need for continued research on the role of media, especially online media, in research dissemination.
Methanomethylophilus alvus Mx1201 provides basis for mutual orthogonal pyrrolysyl tRNA/aminoacyl-tRNA synthetase pairs in mammalian cells
Authors: Meineke Birthe , Heimgärtner Johannes , Lafranchi Lorenzo , Elsässer Simon J 
Published: July 2018

ABSTRACTGenetic code expansion via stop codon suppression is a powerful technique for engineering proteins in mammalian cells with site-specifically encoded non-canonical amino acids (ncAAs). Current methods rely on very few available tRNA/aminoacyl-tRNA synthetase pairs orthogonal in mammalian cells, the pyrrolysyl tRNA/aminoacyl-tRNA synthetase pair from Methanosarcina mazei (Mma PylRS/PylT) being the most active and versatile to date. We found a previously uncharacterized pyrrolysyl tRNA/aminoacyl-tRNA synthetase pair from the human gut archaeon Methanomethylophilus alvus Mx1201 (Mx1201 PylRS/PylT) to be active and orthogonal in mammalian cells. We show that the new PylRS enzyme can be engineered to expand its ncAA substrate spectrum. We find that due to the large evolutionary distance of the two pairs, Mx1201 PylRS/PylT is partially orthogonal to Mma PylRS/PylT. Through rational mutation of Mx1201 PylT, we abolish its non-cognate interaction with Mma PylRS, creating two mutually orthogonal PylRS/PylT pairs. Combined in the same cell, we show that the two pairs can site-selectively introduce two different ncAAs in response to two distinct stop codons. Our work expands the repertoire of mutually orthogonal tools for genetic code expansion in mammalian cells and provides the basis for advanced in vivo protein engineering applications for cell biology and protein production.
ERNIE: A Data Platform for Research Assessment
Authors: Keserci Samet , Davey Avon , Pico Alexander R. , Korobskiy Dmitriy , Chacko George 
Published: July 2018

AbstractData mining coupled to network analysis has been successfully used to study relationships between basic discovery and translational applications such as drug development; and to document research collaborations and knowledge flows. Assembling relevant data for such studies in a form that supports analysis presents challenges. We have developed Enhanced Research Network Information Environment (ERNIE), an open source, scalable cloud-based platform that (i) integrates data drawn from public and commercial sources (ii) provides users with analytical workflows that incorporate expert input at critical stages. A modular design enables the addition, deletion, or substitution of data sources. To demonstrate the capabilities of ERNIE, we have conducted case studies that span drug development and pharmacogenetics. In these studies, we analyze data from regulatory documents, bibliographic and patent databases, research grant records, and clinical trials, to document collaborations and identify influential research accomplishments.
Neural dynamics of associative learning during human sleep
Authors: Canales-Johnson Andrés F. , Merlo Emiliano , Bekinschtein Tristan A. , Arzi Anat 
Published: July 2018

AbstractRecent evidence indicate that humans can learn entirely new information during sleep. To elucidate the neural dynamics underlying sleep-learning we investigated brain activity during auditory-olfactory discriminatory associative learning in human sleep. We found that learning-related delta and sigma neural changes are involved in early acquisition stages, when new associations are being formed. In contrast, learning-related theta activity emerged in later stages of the learning process, after tone-odour associations were already established. These findings suggest that learning new associations during sleep is signalled by a dynamic interplay between slow-waves, sigma and theta activity.
Quantifying the contribution of four resistance mechanisms to ciprofloxacin minimum inhibitory concentration inEscherichia coli: a systematic review
Authors: van der Putten Boas C.L. , Remondini Daniel , Pasquini Giovanni , Janes Victoria A. , Matamoros Sébastien , Schultsz Constance 
Published: July 2018

SynopsisIntroductionCiprofloxacin resistance inEscherichia coliis widespread and adds to the burden ofE. coliinfections. Reviews assessing the genetic basis of ciprofloxacin resistance have mostly been qualitative. However, to allow for the prediction of a resistance phenotype of clinical relevance based on genotypic characteristics, it is essential to quantify the contribution of prevalent genotypic determinants to resistance. We carried out a systematic review to assess the relative contribution of currently known genomic resistance determinants to the minimum inhibitory concentration (MIC) of ciprofloxacin inE. coli.MethodsPubMed and Web of Science were searched for English language studies that assessed both ciprofloxacin MIC and the presence or introduction of genetic determinants of ciprofloxacin resistance inE. coli. We included experimental and observational studies without time restrictions. Medians and ranges of MIC fold changes were calculated for each resistance determinant and for combinations of determinants.ResultsWe included 66 studies, describing 604E. coliisolates that carried at least one genetic resistance determinant. Genes coding for targets of ciprofloxacin (gyrAandparC) are strongest contributors to ciprofloxacin resistance, with median MIC fold increases ranging from 24 (range 4-133) for single Ser83Leu (gyrA) mutants to 1533 (range 256-8533) for triple Ser83Leu, Asp87Asn/Gly (gyrA) and Ser80Ile/Arg (parC) mutants. Other resistance mechanisms, including efflux, physical blocking or enzymatic modification, conferred smaller increases in ciprofloxacin MIC (median MIC fold increases typically around 15, range 1-125). However, the (combined) presence of these other resistance mechanisms further increases resistance with median MIC fold increases of up to 4000, and even in the absence ofgyrAandparCmutations up to 250.ConclusionThis report provides a comprehensive and quantitative overview of the contribution of different genomic determinants to ciprofloxacin resistance inE. coli. Additionally, the data demonstrate the complexity of resistance phenotype prediction from genomic data and could serve as a reference point for studies aiming to address ciprofloxacin resistance prediction using genomics, inE. coli.
Translation Attenuation by Minocycline Increases Lifespan and Improves Proteostasis in Old Post-Stress-Responsive Organisms
Authors: Solis Gregory M. , Kardakaris Rozina , Valentine Elizabeth R. , Bar-Peled Liron , Chen Alice L. , Blewett Megan M. , McCormick Mark A. , Williamson James R. , Kennedy Brian K. , Cravatt Benjamin F. , Petrascheck Michael 
Published: July 2018

SummaryAging impairs the activation of Stress Signaling Pathways (SSPs), preventing the induction of longevity mechanisms late in life. Here we show that the antibiotic minocycline increases lifespan and reduces protein aggregation even in old, SSP-deficient C. elegans by targeting cytoplasmic ribosomes, preferentially attenuating translation of highly translated mRNAs. In contrast to most other longevity paradigms, minocycline inhibits rather than activates all major SSPs and extends lifespan in mutants deficient in the activation of SSPs, lysosomal or autophagic pathways. We propose that minocycline lowers the concentration of newly synthesized aggregation-prone proteins, resulting in a relative increase in protein-folding capacity without the necessity to induce protein-folding pathways. Our study suggests that in old individuals with incapacitated SSPs or autophagic pathways, pharmacological attenuation of cytoplasmic translation is a promising strategy to reduce protein aggregation. Altogether, it provides a geroprotecive mechanism for the many beneficial effects of tetracyclines in models of neurodegenerative disease.
TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes
Authors: Kim Seungill , Cheong Kyeongchae , Park Jieun , Kim Myung-Shin , Kim Ji-Hyun , Seo Min-Ki , Kwon Sun-Ho , Kim Yong-Min , Koo Namjin , Kim Kwang-Soo , Oh Nuri , Kim Ki-Tae , Jeon Jongbum , Kim Hyunbin , Lee Yoon-Young , Sohn Kee Hoon , McCann Honour C , Ye Sang-Kyu , Park Kyung-Soon , Lee Yong-Hwan , Choi Doil 
Published: July 2018

AbstractWhole genome annotation errors that omit essential protein-coding genes hinder further research. We developed Target Gene Family Finder (TGFam-Finder), an optimal tool for structural annotation of protein-coding genes containing target domain(s) of interest in eukaryotic genomes. Large-scale re-annotation of 100 publicly available eukaryotic genomes led to the discovery of essential genes that were missed in previous annotations. An average of 117 (346%) and 148 (45%) additional FAR1 and NLR genes were newly identified in 50 plant genomes. Furthermore, 117 (47%) additional C2H2 zinc finger genes were detected in 50 animal genomes including human and mouse. Accuracy of the newly annotated genes was validated by RT-PCR and cDNA sequencing in human, mouse and rice. In the human genome, 26 newly annotated genes were identical with known functional genes. TGFam-Finder along with the new gene models provide an optimized platform for unbiased functional and comparative genomics and comprehensive evolutionary study in eukaryotes.
Spatial frequency tuning of perceptual learning and transfer in global motion
Authors: Asher Jordi M , Romei Vincenzo , Hibbard Paul B 
Published: July 2018

AbstractPerceptual learning is typically highly specific to the stimuli and task used during training. However, recently it has been shown that training on global motion can transfer to untrained tasks, reflecting the generalising properties of mechanisms at this level of processing. We investigated a) if feedback was required for learning when using an equivalent noise global motion coherence task, and b) the transfer across spatial frequency of training on a global motion coherence task, and the transfer of this training to a measure of contrast sensitivity. For our first experiment two groups, with and without feedback, trained for ten days on a broadband global motion coherence task. Results indicated that feedback was a requirement for learning. For the second experiment training consisted of five days of direction discrimination on one of three global motion tasks (broadband, low or high frequency random-dot Gabors), with trial-by-trial auditory feedback. A pre- and post-training assessment was also conducted, consisting of all three types of global motion stimuli (without feedback) and high and low spatial frequency contrast sensitivity. We predicted that if learning and transfer is cortically localised, then transfer would show specificity to the area processing the task (global motion). In this case, we would predict a broad transfer between spatial frequency conditions of global motion only. However, if transfer occurred as a result of backward generalisation, a more selective transfer would occur matching the low-pass broadband tuning of the area processing global motion. Our training paradigm was successful at eliciting improvement in the trained tasks over the five days. However, post-training transfer to trained or untrained tasks was only reported for the low spatial frequency trained group. This group exhibited increased sensitivity to low spatial frequency contrast, and an improvement for the broadband global motion condition. Our findings suggest that the feedback projections from global to local stages of processing play a role in transfer.
Challenges in assessing the roles of nepotism and reciprocity in cooperation networks
Authors: Carter Gerald G. , Schino Gabriele , Farine Damien 
Published: July 2018

AbstractNepotism and reciprocity are not mutually exclusive explanations for cooperation, because helping decisions can depend on both kinship cues and past reciprocal help. The importance of these two factors can therefore be difficult to disentangle using observational data. We developed a resampling procedure for inferring the statistical power to detect observational evidence of nepotism and reciprocity. We first applied this procedure to simulated datasets resulting from perfect reciprocity, where the probability and duration of helping events from individual A to B equaled that from B to A. We then assessed how the probability of detecting correlational evidence of reciprocity was influenced by (1) the number of helping observations and (2) varying degrees of simultaneous nepotism. Last, we applied the same analysis to empirical data on food sharing in vampire bats and allogrooming in mandrills and Japanese macaques. We show that at smaller sample sizes, the effect of kinship was easier to detect and the relative role of kinship was overestimated compared to the effect of reciprocal help in both simulated and empirical data, even with data simulating perfect reciprocity and imperfect nepotism. We explain the causes and consequences of this difference in power for detecting the roles of kinship versus reciprocal help. To compare the relative importance of genetic and social relationships, we therefore suggest that researchers measure the relative reliability of both coefficients in the model by plotting these coefficients and their detection probability as a function of sampling effort. We provide R scripts to allow others to do this power analysis with their own datasets.
YB-1 IS REQUIRED FOR THE GENESIS AND METASTATIC CAPACITY OF HUMAN BREAST CANCER
Authors: Lefort Sylvain , El-Naggar Amal , Tan Susanna , Colborne Shane , Negri Gian Luca , Pellacani Davide , Hirst Martin , Gusterson Barry , Morin Gregg B. , Sorensen Poul H. , Eaves Connie J. 
Published: July 2018

ABSTRACTBreast cancer heterogeneity has made it challenging to elucidate shared mechanisms that underpin properties that are critical to their growthin vivo. Here, we interrogate the role of YB-1 protein in thein vivotumorigenic activity ofde novowell as cell line models of human breast cancer. Short-hairpin RNA-mediated knockdown of YB-1 in MDA-MB-231 cells blocked both their local tumour-forming and lung-colonizing activity in transplanted immunodeficient mice. YB-1 knockdown also revealed its important role at early stages of human mammary cell transformation in the generation of invasive ductal carcinoma and ductal carcinomain situproduced in mice transplanted with freshly isolated human mammary cells transduced, respectively, withKRASG12D, or myristoylated-AKT1. Conversely, upregulated expression of YB-1 in the poorly tumorigenic T47D cells enhanced this activity. Mechanistically, reducing YB-1 levels in MDA-MB-231 cells impaired their induction of HIF1α, and G3BP1, known YB-1 translational targets and key elements of a stress-adaptive program.
The distribution of large floating seagrass (Zostera marina) clumps in northern temperate zones of Bohai Bay in the Bohai Sea, China
Authors: Min Xu , Yi Zhou , Tao Zhang , Yun-Ling Zhang 
Published: July 2018

AbstractSeagrass meadows (Zostera marina) are important coastal ecosystems with high levels of productivity and biodiversity. They are subject to considerable natural and anthropogenic threats in China, such as oyster and snail aquaculture, wastewater discharge, electro-fishing, shellfish collection, typhoons and floods. When seagrass communities are disturbed, they can become removed from the sediment and converted into floating clumps, which then serve as marine hot spots attracting a variety of marine organisms that then inhabit them. They are important nursery habitats for many economic fish such as red drum (Sciaenops ocellatus), Atlantic cod (Gadus morhua), queen conch (Strombus gigas), and blue crab (Callinectes sapidus). Thus, it is necessary to study the distribution and biological characteristics of these floating seagrass clumps. In September 2016 we observed large scale floating Z. marina clumps in the northernmost area of Bohai Bay (38°57’1.14”−39° 0’41.28” N, 118°45’23.22”−118°47’6.96” E), in the Bohai Sea, China. We observed characteristics that precluded their origination from the nearby Caofeidian seagrass meadows. Two research cruises were undertaken, during which we did not observe other marine organisms accompanying these floating Z. marina clumps. The dominant frond lengths were 40–50 cm, with less than 5% of the total number of fronds found in larger size categories (80–90 and 90–100 cm). We aim to pursue future research into the breakdown and dislodgement characteristics of Z. marina clumps and the processes whereby they sink and integrate with the sediment.