bluuebunny/crossref_metadata_2025 huggingface dataset:
“This dissonance”
Authors: Bordet Geneviève
Published: November 2018

Writing a convincing abstract requires the ability to demonstrate credibility through an adequate selection of
keywords. A case in point is the selection of shell nouns determined by this. Based on a comparable
interdisciplinary corpus of 400 PhD abstracts written in English by writers in an Anglophone and a Francophone
context, the role of shell nouns determined by this is studied to (1) assess their impact on textual
cohesion (2) evaluate the connection between the selected terms and the discipline’s epistemological values as
perceived by newcomers (3) consider the influence of the writer’s linguistic origin on the handling of this device.
This study aims to contribute to the assessment of the parameters which might undermine writers’ credibility in their
scientific community.
Asserting research status, values and relevance in thesis abstracts of Science and Engineering
Authors: Mehrjooseresht Maryam , Ahmad Ummul K.
Published: November 2018

This study examines the use of evaluation in thesis abstracts written by Malaysian novice research writers from Science
and Engineering fields. Different linguistic features performing three different functions of evaluation were
identified and categorised into status, value and relevance. Lexico-grammatical analysis has shown variations in terms
of the overall preferences for status over value and relevance in the two fields. Science writers were more inclined
to include status markers expressing certainty while summarising their research findings in the Product section of
abstracts whereas Engineering writers appeared less assertive. Results from this study offer L2 research writers
insights into specific linguistic choices to be made for writing efficient and persuasive research abstracts.
Chinese writers of English RAs as creators of a research space in a national context
Authors: Chen Xinren
Published: November 2018

Based on Swales’ (1990, 2004) CARS
model, this study examines 95 research articles (RAs) published by Chinese English-language writers doing Applied
Linguistics across three periods of time to find out whether and to what extent they move over time towards the
conventional construction of the identity as creators of a research space in the introductory part of their RAs
published in a national context. The findings confirm the occurrence of the diachronic change, which is ascribed to
the accrued influence of international academic conventions on Chinese English-language writers. Hopefully, this study
can help improve the teaching and writing of RA Introductions for the purposes of English-language international
publication and enrich existing research on identity construction in academic discourse.
Conference abstracts in English
Authors: Povolná Renata
Published: November 2018

With the growing internationalisation of all scholarship the use of English as an international lingua franca has
become an important prerequisite for scholars who intend to submit their abstracts and present their research to an
academic audience at international conferences. Consequently, scholars from non-Anglophone backgrounds have to master
the writing of this research-process genre (Swales, 1990) in English, since
otherwise they may risk being refused participation at conferences and publication in conference proceedings. This
chapter analyses the textual organisation of conference abstracts (CAs) written in English with the aim of finding out
whether there is intercultural variation in rhetorical moves and their linguistic realisations applied by Anglophone
scholars and those from some countries where Slavonic languages are spoken.
Not the same, but how different?
Authors: Murillo Silvia
Published: November 2018

Reformulation markers can be considered indicators of rhetorical conventions (Cuenca, 2003). In this paper I contrast these markers in the SciELF corpus of unedited research papers
(building on previous work [Murillo, submitted]) and in a comparable ENL
(English as a Native Language) corpus (SERAC), focusing on the overall frequency, the relative frequency of each
marker and the discourse processes they introduce (Murillo, 2012). The
results reveal statistically significant differences between the two corpora regarding the specific choice of
reformulation markers and the processes introduced by them. Further, the “similects” of the SciELF corpus (Mauranen, 2012) present very different trends. ELF does not seem to constitute
a homogeneous use of the English language, at least at the lexico-grammatical level.
Elements of denial in Capeverdean
Authors: Pratas Fernanda
Published: November 2018

This paper aims at showing that Capeverdean, a Portuguese-based Creole, is a strict Negative Concord language. In fact, n-words (Laka 1990) like ningen ‘no.one’ and nada ‘nothing’ always co-occur with sentential negation, be they in preverbal or postverbal position. This means that they are prohibited in all non-negative clauses, including modal contexts. Syntactically, they show a behavior typical of weak Negative Polarity Items (NPIs) as described in Martins (2000). Following Giannakidou (2002), I propose that, semantically, these n-words are universal quantifiers with no intrinsic negative meaning. Finally, I briefly address the adverbs tioxi and nunka, which roughly mean ‘never’: the former is also a weak NPI but not a quantifier, the latter may be ambiguous between a strong and a weak NPI, and seems a quantifier.
Bayesian generalized biclustering analysis via adaptive structured shrinkage
Authors: Li Ziyi , Chang Changgee , Kundu Suprateek , Long Qi
Published: November 2018

Biclustering techniques can identify local patterns of a data matrix by clustering feature space and sample space at the same time. Various biclustering methods have been proposed and successfully applied to analysis of gene expression data. While existing biclustering methods have many desirable features, most of them are developed for continuous data and few of them can efficiently handle -omics data of various types, for example, binomial data as in single nucleotide polymorphism data or negative binomial data as in RNA-seq data. In addition, none of existing methods can utilize biological information such as those from functional genomics or proteomics. Recent work has shown that incorporating biological information can improve variable selection and prediction performance in analyses such as linear regression and multivariate analysis. In this article, we propose a novel Bayesian biclustering method that can handle multiple data types including Gaussian, Binomial, and Negative Binomial. In addition, our method uses a Bayesian adaptive structured shrinkage prior that enables feature selection guided by existing biological information. Our simulation studies and application to multi-omics datasets demonstrate robust and superior performance of the proposed method, compared to other existing biclustering methods.
The Superficial White Matter in Autism and Its Role in Connectivity Anomalies and Symptom Severity
Authors: Hong Seok-Jun , Hyung Brian , Paquola Casey , Bernhardt Boris C
Published: November 2018

In autism spectrum disorders (ASDs), the majority of neuroimaging studies have focused on the analysis of cortical morphology. White matter changes remain less understood, particularly their association to cortical structure and function. Here, we focused on region that has gained only little attention in ASD neuroimaging: the superficial white matter (SWM) immediately beneath the cortical interface, a compartment playing a prominent role in corticogenesis that incorporates long- and short-range fibers implicated in corticocortical connectivity. Studying a multicentric dataset of ASD and neurotypical controls, we harnessed surface-based techniques to aggregate microstructural SWM diffusion features. Multivariate analysis revealed SWM anomalies in ASD compared with controls in medial parietal and temporoparietal regions. Effects were similar in children and adolescents/adults and consistent across sites. Although SWM anomalies were more confined when correcting for cortical thickness and surface area, findings were overall robust. Diffusion anomalies modulated functional connectivity reductions in ASD and related to symptom severity. Furthermore, mediation models indicated a link between SWM changes, functional connectivity, and symptom load. Analyses targeting the SWM offer a novel perspective on the interplay between structural and functional network perturbations in ASD, highlighting a potentially important neurobiological substrate contributing to its diverse behavioral phenotype.
Ontological Security, Civilian Power, and German Foreign Policy Toward Russia1
Authors: Eberle Jakub , Handl Vladimír
Published: November 2018

The article analyzes Germany's policies toward Russia from an ontological security perspective. We argue that foreign policy should be seen as a tool that allows states to maintain a sense of a reasonably stable self, which enables them to cope in the changing world. We develop a three-layered model conceptualizing ontological security through narratives about the self, a significant other, and the international system and show its particular relevance for explicating policy change. When threatened by a crisis, states respond by narrative adjustment that highlights continuity on some levels, while enabling change on other levels. Developing the argument that Germany's ontological security is based in the “civilian power” narrative, we use our model to reconstruct Germany's response to Russia's wars in Georgia and Ukraine. In both cases, the discourse highlighted the ongoing validity of civilian power on the level of the international order, while challenges were accommodated by adjustments on the level of the self and the significant other. Ontological security was restored vis-à-vis the changing world by reinforcing the civilian power as a norm, while shifting blame to either both Germany and Russia (2008), or Russia exclusively (2014), for not adhering to it at a given time.
Incorporating a location-based socioeconomic index into a de-identified i2b2 clinical data warehouse
Authors: Gardner Bret J , Pedersen Jay G , Campbell Mary E , McClay James C
Published: November 2018

Objective

Clinical research data warehouses are largely populated from information extracted from electronic health records (EHRs). While these data provide information about a patient’s medications, laboratory results, diagnoses, and history, her social, economic, and environmental determinants of health are also major contributing factors in readmission, morbidity, and mortality and are often absent or unstructured in the EHR. Details about a patient’s socioeconomic status may be found in the U.S. census. To facilitate researching the impacts of socioeconomic status on health outcomes, clinical and socioeconomic data must be linked in a repository in a fashion that supports seamless interrogation of these diverse data elements. This study demonstrates a method for linking clinical and location-based data and querying these data in a de-identified data warehouse using Informatics for Integrating Biology and the Bedside.

Materials and Methods

Patient data were extracted from the EHR at Nebraska Medicine. Socioeconomic variables originated from the 2011-2015 five-year block group estimates from the American Community Survey. Data querying was performed using Informatics for Integrating Biology and the Bedside. All location-based data were truncated to prevent identification of a location with a population <20 000 individuals.

Results

We successfully linked location-based and clinical data in a de-identified data warehouse and demonstrated its utility with a sample use case.

Discussion

With location-based data available for querying, research investigating the impact of socioeconomic context on health outcomes is possible. Efforts to improve geocoding can readily be incorporated into this model.

Conclusion

This study demonstrates a means for incorporating and querying census data in a de-identified clinical data warehouse.
Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review
Authors: Koleck Theresa A , Dreisbach Caitlin , Bourne Philip E , Bakken Suzanne
Published: November 2018

Objective

Natural language processing (NLP) of symptoms from electronic health records (EHRs) could contribute to the advancement of symptom science. We aim to synthesize the literature on the use of NLP to process or analyze symptom information documented in EHR free-text narratives.

Materials and Methods

Our search of 1964 records from PubMed and EMBASE was narrowed to 27 eligible articles. Data related to the purpose, free-text corpus, patients, symptoms, NLP methodology, evaluation metrics, and quality indicators were extracted for each study.

Results

Symptom-related information was presented as a primary outcome in 14 studies. EHR narratives represented various inpatient and outpatient clinical specialties, with general, cardiology, and mental health occurring most frequently. Studies encompassed a wide variety of symptoms, including shortness of breath, pain, nausea, dizziness, disturbed sleep, constipation, and depressed mood. NLP approaches included previously developed NLP tools, classification methods, and manually curated rule-based processing. Only one-third (n = 9) of studies reported patient demographic characteristics.

Discussion

NLP is used to extract information from EHR free-text narratives written by a variety of healthcare providers on an expansive range of symptoms across diverse clinical specialties. The current focus of this field is on the development of methods to extract symptom information and the use of symptom information for disease classification tasks rather than the examination of symptoms themselves.

Conclusion

Future NLP studies should concentrate on the investigation of symptoms and symptom documentation in EHR free-text narratives. Efforts should be undertaken to examine patient characteristics and make symptom-related NLP algorithms or pipelines and vocabularies openly available.
How scientists can take the lead in establishing ethical practices for social media research
Authors: Pagoto Sherry , Nebeker Camille
Published: November 2018

Social media use has become ubiquitous in the United States, providing unprecedented opportunities for research. However, the rapidly evolving research landscape has far outpaced federal regulations for the protection of human subjects. Recent highly publicized scandals have raised legitimate concerns in the media about how social media data are being used. These circumstances combined with the absence of ethical standards puts even the best intentioned scientists at risk of possible research misconduct. The scientific community may need to lead the charge in insuring the ethical use of social media data in scientific research. We propose 6 steps the scientific community can take to lead this charge. We underscore the important role of funding agencies and universities to create the necessary ethics infrastructure to allow social media research to flourish in a way that is pro-technology, pro-science, and most importantly, pro-humanity.
The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine
Authors: Berger Kathryn A , Pigott David M , Tomlinson Francesca , Godding David , Maurer-Stroh Sebastian , Taye Biruhalem , Sirota Fernanda L , Han Alvin , Lee Raphael T C , Gunalan Vithiagaran , Eisenhaber Frank , Hay Simon I , Russell Colin A
Published: November 2018

Background

Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

Methods

We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities.

Results

Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively.

Conclusions

Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.
Chronic aspects of leprosy—neglected but important
Authors: Lockwood Diana N J
Published: November 2018

The chronic aspects of leprosy are discussed here. They are a consequence of the peripheral nerve damage that affects many patients during their lifetime with leprosy. The peripheral nerve damage leaves people unable to feel and with weakness in their hands and feet. They are at risk of damaging their hands and feet, causing the disabilities and deformities that characterise late leprosy.

More than 200 000 new leprosy patients are diagnosed globally each year. Better data are needed from cohort studies to estimate the number of patients developing nerve damage and modelling studies are needed to estimate the number of patients who develop disabilities. For some of them, this will be a lifelong disability.

Nerve damage is caused by inflammation in leprosy-affected nerves. Patients with nerve damage of <6-mo duration need treatment with steroids. About 66% of multibacillary patients will develop nerve damage. Plastic graded monofilaments can be used to detect nerve damage in leprosy and diabetic clinics. Assessing nerve damage and treating patients with steroids in leprosy programmes needs to be strengthened. The World Health Organization has a successful programme for supplying antibiotics for treating leprosy infection to national leprosy programmes. They should take responsibility for providing steroids to national programmes since this is a core part of the treatment for >66% of multibacillary patients. Patients need to be asked about neuropathic pain symptoms and treated if necessary.

Treated leprosy patients are at risk of developing ulcers in their feet. Treatment and prevention needs to be improved through health education, providing protective footwear and patient empowerment.
Convergent Evolution of Effector Protease Recognition byArabidopsisand Barley
Authors: Carter Morgan E. , Helm Matthew , Chapman Antony V. E. , Wan Emily , Restrepo Sierra Ana Maria , Innes Roger W. , Bogdanove Adam J. , Wise Roger P.
Published: November 2018

The Pseudomonas syringae cysteine protease AvrPphB activates the Arabidopsis resistance protein RPS5 by cleaving a second host protein, PBS1. AvrPphB induces defense responses in other plant species, but the genes and mechanisms mediating AvrPphB recognition in those species have not been defined. Here, we show that AvrPphB induces defense responses in diverse barley cultivars. We also show that barley contains two PBS1 orthologs, that their products are cleaved by AvrPphB, and that the barley AvrPphB response maps to a single locus containing a nucleotide-binding leucine-rich repeat (NLR) gene, which we termed AvrPphB Response 1 (Pbr1). Transient coexpression of PBR1 with wild-type AvrPphB but not with a protease inactive mutant triggered defense responses, indicating that PBR1 detects AvrPphB protease activity. Additionally, PBR1 coimmunoprecipitated with barley and Nicotiana benthamiana PBS1 proteins, suggesting mechanistic similarity to detection by RPS5. Lastly, we determined that wheat cultivars also recognize AvrPphB protease activity and contain two putative Pbr1 orthologs. Phylogenetic analyses showed, however, that Pbr1 is not orthologous to RPS5. Our results indicate that the ability to recognize AvrPphB evolved convergently and imply that selection to guard PBS1-like proteins occurs across species. Also, these results suggest that PBS1-based decoys may be used to engineer protease effector recognition–based resistance in barley and wheat.
Comprehensive Disease Survey of U.S. Sunflower: Disease Trends, Research Priorities and Unanticipated Impacts
Authors: Gulya Thomas , Harveson Robert , Mathew Febina , Block Charles , Thompson Sue , Kandel Hans , Berglund Duane , Sandbakken John , Kleingartner Larry , Markell Samuel
Published: November 2018

Between 2002 and 2015, a comprehensive survey of sunflower fields across seven Midwestern U.S. states was conducted 12 times and continues to be conducted every other year. The surveyors collected data on yield, agronomic management factors, disease, insect, weed, and bird damage. All surveyors were volunteers and came from universities (extension and research staff), USDA-ARS, and seed and chemical companies. In the 12 years the survey was conducted, data from 2,267 fields were collected. The results are presented annually at the National Sunflower Association Research Forum and are used to set sunflower research priorities. While 10 diseases are surveyed annually, we focus this article on the importance, findings, implications, and impacts of the five most important: downy mildew, Phomopsis stem canker, rust, Rhizopus head rot, and Sclerotinia head rot. This survey is unique among field crops in both scope and scale, and this manuscript discusses salient and clandestine benefits of intense and long-term disease surveys.
Population Subdivision and the Frequency of Aflatoxigenic Isolates in Aspergillus flavus in the United States
Authors: Drott Milton T. , Fessler Lauren M. , Milgroom Michael G.
Published: November 2018

Consumption of food contaminated with aflatoxin, from crops infected by Aspergillus flavus, is associated with acute toxicosis, cancer, and stunted growth. Although such contamination is more common in the lower latitudes of the United States, it is unclear whether this pattern is associated with differences in the relative frequencies of aflatoxigenic individuals of A. flavus. To determine whether the frequency of the aflatoxin-producing ability of A. flavus increases as latitude decreases, we sampled 281 isolates from field soils in two north-south transects in the United States and tested them for aflatoxin production. We also genotyped 161 isolates using 10 microsatellite markers to assess population structure. Although the population density of A. flavus was highest at lower latitudes, there was no difference in the frequency of aflatoxigenic A. flavus isolates in relation to latitude. We found that the U.S. population of A. flavus is subdivided into two genetically differentiated subpopulations that are not associated with the chemotype or geographic origin of the isolates. The two populations differ markedly in allelic and genotypic diversity. The less diverse population is more abundant and may represent a clonal lineage derived from the more diverse population. Overall, increased aflatoxin contamination in lower latitudes may be explained partially by differences in the population density of A. flavus, not genetic population structure.
Host-pathogen coevolution increases genetic variation in susceptibility to infection
Authors: Duxbury Elizabeth ML , Day Jonathan P , Vespasiani Davide Maria , Thüringer Yannik , Tolosana Ignacio , Smith Sophia CL , Tagliaferri Lucia , Kamacioglu Altug , Lindsley Imogen , Love Luca , Unckless Robert L , Jiggins Francis M , Longdon Ben
Published: November 2018

It is common to find considerable genetic variation in susceptibility to infection in natural populations. We have investigated whether natural selection increases this variation by testing whether host populations show more genetic variation in susceptibility to pathogens that they naturally encounter than novel pathogens. In a large cross-infection experiment involving four species ofDrosophilaand four host-specific viruses, we always found greater genetic variation in susceptibility to viruses that had coevolved with their host. We went on to examine the genetic architecture of resistance in one host species, finding that there are more major-effect genetic variants in coevolved host-parasite interactions. We conclude that selection by pathogens increases genetic variation in host susceptibility, and much of this effect is caused by the occurrence of major-effect resistance polymorphisms within populations.
Cell assemblies in the cortico-hippocampal-reuniens network during slow oscillations
Authors: Angulo-Garcia David , Ferraris Maëva , Ghestem Antoine , Nallet-Khosrofian Lauriane , Bernard Christophe , Quilichini Pascale P
Published: November 2018

The nucleus reuniens (NR) is an important anatomical and functional relay between the medial prefrontal cortex (mPFC) and the hippocampus (HPC). Whether the NR controls neuronal assemblies, a hallmark of information exchange between the HPC and mPFC for memory transfer/consolidation, is not known. Using simultaneous LFP and unit recordings in NR, HPC and mPFC in rats during slow oscillations under anesthesia, we identified a reliable sequential activation of NR neurons at the beginning of UP states, which preceded mPFC ones. NR sequences were spatially organized, from dorsal to ventral NR. Chemical inactivation of the NR disrupted mPFC sequences at the onset of UP states as well as HPC sequences present during sharp-wave ripples. We conclude that the NR contributes to the coordination and stabilization of mPFC and HPC neuronal sequences during slow oscillations, possibly via the early activation of its own sequences.

Significance Statement

Neuronal assemblies are believed to be instrumental to code/encode/store information. They can be recorded in different brain regions, suggesting that widely distributed networks of networks are involved in such information processing. The prefrontal cortex, the hippocampus and the thalamic nucleus reuniens constitute a typical example of a complex network involved in memory consolidation. In this study, we show that spatially organized cells assemblies are recruited in the nucleus reuniens at the UP state onset during slow oscillations. Nucleus reuniens activity appears to be necessary to the stability of prefrontal cortex and hippocampal cell assembly formation during slow oscillations. This result further highlights the role of the Nucleus Reuniens as a functional hub for exchanging and processing memories.
T cells instruct dendritic cells to produce inflammasome independent IL-1β causing systemic inflammation
Authors: Jain Aakanksha , Irizarry-Caro Ricardo A. , Chawla Amanpreet S. , Philip Naomi H. , Carroll Kaitlin R. , Katz Jonathan D. , Oberst Andrew , Chervonsky Alexander V. , Pasare Chandrashekhar
Published: November 2018

While IL-1β is critical for anti-microbial host defense, it is also a key mediator of autoimmune inflammation. Inflammasome activation following pathogenic insults is known to result in IL-1β production. However, the molecular events that produce IL-1β during T cell driven autoimmune diseases remain unclear. Here, we have discovered an inflammasome-independent pathway of IL-1β production that is triggered upon cognate interactions between dendritic cells and effector CD4 T cells. Analogous to inflammasome activation, this “T cell-instructed IL-1β also relies on two independent signaling events. TNFα produced by activated CD4 T cells engages TNFR signaling on DCs leading to pro-IL-1β synthesis. Subsequently, FasL, also expressed by effector CD4 T cells, engages Fas on DCs leading to caspase-8 dependent pro-IL-1β cleavage. Remarkably, this two-step mechanism is completely independent of pattern recognition receptor activation. IL-1β produced upon cognate DC-effector CD4 T cell interaction causes wide spread leukocyte infiltration, a hallmark of systemic inflammation as well as autoimmune pathology. This study has uncovered a novel feature of DC-T cell cross-talk that allows for active IL-1β secretion independent of innate sensing pathways and provides a mechanistic explanation for IL-1β production and its downstream consequences in CD4 T cell driven autoimmune pathology.
Cellular Dynamics and Genomic Identity of Centromeres in the Cereal Blast Fungus
Authors: Yadav Vikas , Yang Fan , Reza Md. Hashim , Liu Sanzhen , Valent Barbara , Sanyal Kaustuv , Naqvi Naweed I.
Published: November 2018

A series of well-synchronized events mediated by kinetochore-microtubule interactions ensure faithful chromosome segregation in eukaryotes. Centromeres scaffold kinetochore assembly and are among the fastest evolving chromosomal loci in terms of the DNA sequence, length, and organization of intrinsic elements. Neither the centromere structure nor the kinetochore dynamics is well studied in plant pathogenic fungi. Here, we sought to understand the process of chromosome segregation in the rice blast fungus,Magnaporthe oryzae. High-resolution confocal imaging of GFP-tagged inner kinetochore proteins, CenpA and CenpC, revealed an unusual albeit transient declustering of centromeres just before anaphase separation inM. oryzae. Strikingly, the declustered centromeres positioned randomly at the spindle midzone without an apparent metaphase plateper se. Using chromatin immunoprecipitation followed by deep sequencing, all seven centromeres were identified as CenpA-rich regions in the wild-type Guy11 strain ofM. oryzae. The centromeres inM. oryzaeare regional and span 57 to 109 kb transcriptionally poor regions. No centromere-specific DNA sequence motif or repetitive elements could be identified in these regions suggesting an epigenetic specification of centromere function inM. oryzae. Highly AT-rich and heavily methylated DNA sequences were the only common defining features of all the centromeres in rice blast fungus. PacBio genome assemblies and synteny analyses facilitated comparison of the centromere regions in distinct isolate(s) of rice blast, wheat blast, and inM. poae.Overall, this study identified unusual centromere dynamics and precisely mapped the centromere DNA sequences in the top model fungal pathogens that belong to theMagnaporthalesand cause severe losses to global production of food crops and turf grasses.

Author summary

Magnaporthe oryzaeis an important fungal pathogen that causes an annual loss of 10-30% of the rice crop due to the devastating blast disease. In most organisms, kinetochores are arranged either in the metaphase plate or are clustered together to facilitate synchronized anaphase separation of chromosomes. In this study, we show that the initially clustered kinetochores separate and position randomly prior to anaphase inM. oryzae. Centromeres, identified as the site of kinetochore assembly, are regional type without any shared sequence motifs inM. oryzae. Together, this study reveals atypical kinetochore dynamics and identifies functional centromeres inM. oryzae, thus paving the way to define heterochromatin boundaries and understand the process of kinetochore assembly on epigenetically specified centromere loci in the economically important cereal blast and summer patch pathogens. This study paves the way for understanding the contribution of heterochromatin in genome stability and virulence of the blast fungus.
Excess light priming in Arabidopsis thaliana genotypes with altered DNA methylomes
Authors: Ganguly Diep R. , Stone Bethany A. B. , Bowerman Andrew F. , Eichten Steven R. , Pogson Barry J.
Published: November 2018

Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant’s ability to respond to future events. A clear example of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes towards stress priming and, consequently, the potential contribution from DNA methylation – a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional ‘dampening’ in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.

One sentence summary

Photoprotection and priming against recurring excess light is functional despite impaired maintenance of the DNA methylome.
Reversing an extracellular electron transfer pathway for electrode-driven NADH generation
Authors: Tefft Nicholas M. , TerAvest Michaela A.
Published: November 2018

Microbial electrosynthesis is an emerging technology with the potential to simultaneously store renewably generated energy, fix carbon dioxide, and produce high-value organic compounds. However, limited understanding of the route of electrons into the cell remains an obstacle to developing a robust microbial electrosynthesis platform. To address this challenge, we engineered an inward electron transfer pathway inShewanella oneidensisMR-1. The pathway uses native Mtr proteins to transfer electrons from an electrode to the inner membrane quinone pool. Subsequently, electrons are transferred from quinones to NAD+by native NADH dehydrogenases. This reverse functioning of NADH dehydrogenases is thermodynamically unfavorable, therefore we have added a light-driven proton pump (proteorhodopsin) to generate proton-motive force to drive this activity. Finally, we use reduction of acetoin to 2,3-butanediol via a heterologous butanediol dehydrogenase (Bdh) as an electron sink. Bdh is an NADH-dependent enzyme, therefore, observation of acetoin reduction supports our hypothesis that cathodic electrons are transferred to intracellular NAD+. Multiple lines of evidence indicate proper functioning of the engineered electrosynthesis system: electron flux from the cathode is influenced by both light and acetoin availability; and 2,3-butanediol production is highest when both light and a poised electrode are present. Using a hydrogenase-deficientS. oneidensisbackground strain resulted in a stronger correlation between electron transfer and 2,3-butanediol production, suggesting that hydrogen production is an off-target electron sink in the wild-type background. This system represents a promising genetically engineered microbial electrosynthesis platform and will enable a new focus on synthesis of specific compounds using electrical energy.
Visual field advantage: Redefined by training?
Authors: Stone Scott A. , Baker Jared , Olsen Rob , Gibb Robbin , Doan Jon , Hoetmer Joshua , Gonzalez Claudia L.R.
Published: November 2018

In 1990, Fred Previc postulated that most peri-personal space interactions occurred in the lower visual field (LVF), leading to an advantage when compared to the upper visual field (UVF). It is not clear if extensive practice can affect the difference between interactions in the LVF/UVF. We tested male and female basketball varsity athletes and non-athletes on a DynaVision D2 visuomotor reaction task. We recruited basketball players because in their training they spend significant amount of time processing upper visual field information. We found a lower visual field advantage in all participants, but this advantage was significantly reduced in the athletes. The results suggest that training can be a powerful modulator of visuomotor function.
Convolutional Sparse Coded Dynamic Brain Functional Connectivity
Authors: Yan Jin , Zhu Yingying
Published: November 2018

Functional brain network has been widely studied in many previous work for brain disorder diagnosis and brain network analysis. However, most previous work focus on static dynamic brain network research. Lots of recent work reveals that the brain shows dynamic activity even in resting state. Such dynamic brain functional connectivity reveals discriminative patterns for identifying many brain disorders. Current sliding window based dynamic brain connectivity framework are not easy to be applied to real clinical applications due to many issues: First, how to set up the optimal sliding window size and how to determine the threshold for the brain connectivity patterns. Secondly, how to represent the high dimensional dynamic brain connectivity pattern in a low dimensional representations for diagnosis purpose. Last, how to deal with the different length dynamic brain network patterns especially when the raw data are of different length. In order to address all those above issues, we proposed a new framework, which employs multiple scale sliding windows and automatically learns a sparse and low ran dynamic brain functional connectivity patterns from raw fMRI data. Furthermore, we are able to measure different length dynamic brain functional connectivity patterns in an equal space by learning a sparse coded convolutional filters. We have evaluated our method with state of the art dynamic brain network methods and the results demonstrated the strong potential of our methods for brain disorder diagnosis in real clinical applications.
Agreement between 18F-Florbetapir PET imaging and cerebrospinal fluid Aβ1-42, Aβ1-40, tTau and pTau measured on the LUMIPULSE G fully automated platform
Authors: Alcolea Daniel , Pegueroles Jordi , Muñoz Laia , Camacho Valle , López-Mora Diego , Fernández-León Alejandro , Bastard Nathalie Le , Huyck Els , Nadal Alicia , Olmedo Verónica , Montal Victor , Vilaplana Eduard , Clarimón Jordi , Blesa Rafael , Fortea Juan , Lleó Alberto
Published: November 2018

INTRODUCTION

The development of fully automated immunoassay platforms has improved the technical reliability of cerebrospinal fluid (CSF) biomarkers for Alzheimer’s disease.

METHODS

We quantified Aβ1-42, Aβ1-40, tTau and pTau levels using the Lumipulse G System in 94 CSF samples from participants of the SPIN cohort with available 18F-Florbetapir imaging. Amyloid scans were assessed visually and through automated quantification. We determined the cutoffs of CSF biomarkers that optimized their agreement with 18F-Florbetapir PET and evaluated concordance between markers of the amyloid category.

RESULTS

Aβ1-42, tTau and pTau (but not Aβ1-40) and the ratios with Aβ1-42 had good diagnostic agreement with 18F-Florbetapir PET. As a marker of amyloid pathology, the Aβ1-42/Aβ1-40 ratio had higher agreement and better correlation with amyloid PET than Aβ1-42 alone.

DISCUSSION

CSF biomarkers measured with the Lumipulse G System show good agreement with amyloid imaging. Combination of Aβ1-42 with Aβ1-40 increases the agreement between markers of amyloid pathology.
Regulation of eIF6 through multisite and sequential phosphorylation by GSK3β
Authors: Jungers Courtney F. , Elliff Jonah M. , Masson-Meyers Daniela S. , Phiel Christopher J. , Origanti Sofia
Published: November 2018

Eukaryotic translation initiation factor 6 is essential for the synthesis of 60S ribosomal subunits and for regulating the association of 60S and 40S subunits. A mechanistic understanding of how eIF6 modulates translation in response to stress, specifically starvation-induced stress, is lacking. Our studies have uncovered a novel mode of eIF6 regulation by GSK3 that is predominantly active in response to serum starvation. Human eIF6 is phosphorylated by GSK3β at a multisite motif in the C-terminus. Sequential phosphorylation by GSK3β requires phosphorylation at a priming site. In response to serum starvation, eIF6 accumulates in the cytoplasm and this altered localization is dependent on GSK3. Disruption of eIF6 phosphorylation enhances translation inhibition and markedly sensitizes the cells to serum starvation. These results suggest that eIF6 regulation by GSK3β contributes to the attenuation of global protein synthesis that is critical for adaptation to starvation-induced stress.
Frontal and parietal alpha oscillations reflect attentional modulation of cross-modal matching
Authors: Misselhorn Jonas , Friese Uwe , Engel Andreas K.
Published: November 2018

Multisensory perception is shaped by both attentional selection of relevant sensory inputs and exploitation of stimulus-driven factors that promote cross-modal binding. Underlying mechanisms of both top-down and bottom-up modulations have been linked to changes in alpha/gamma dynamics in primary sensory cortices and temporoparietal cortex. Accordingly, it has been proposed that alpha oscillations provide pulsed inhibition for gamma activity and thereby dynamically route cortical information flow. In this study, we employed a recently introduced multisensory paradigm incorporating both bottom-up and top-down aspects of cross-modal attention in an EEG study. The same trimodal stimuli were presented in two distinct attentional conditions, focused on visual-tactile or audio-visual components, for which cross-modal congruence of amplitude changes had to be evaluated. Neither top-down nor bottom-up cross-modal attention modulated alpha or gamma power in primary sensory cortices. Instead, we found alpha band effects in bilateral frontal and right parietal cortex. We propose that frontal alpha oscillations reflect the origin of top-down control regulating perceptual gains and that modulations of parietal alpha oscillations relates to intersensory re-orienting. Taken together, we suggest that the idea of selective cortical routing via alpha oscillations can be extended from sensory cortices to the frontoparietal attention network.
Population genome sequencing of the scab fungal speciesVenturia inaequalis,Venturia pirina,Venturia aucupariaeandVenturia asperata
Authors: Cam Bruno Le , Sargent Dan , Gouzy Jérôme , Amselem Joëlle , Bellanger Marie-Noëlle , Bouchez Olivier , Brown Spencer , Caffier Valérie , Gracia Marie De , Debuchy Robert , Duvaux Ludovic , Payen Thibaut , Sannier Mélanie , Shiller Jason , Collemare Jérôme , Lemaire Christophe
Published: November 2018

TheVenturiagenus comprises fungal species that are pathogens onRosaceaehost plants, includingV. inaequalisandV. asperataon apple,V. aucupariaeon sorbus andV. pirinaon pear. Although the genetic structure ofV. inaequalispopulations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87Venturiastrains that represent each species and each population withinV. inaequalis. We present a PacBio genome assembly for theV. inaequalisEU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies ofV. inaequalisandV. aucupariaecontain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly ofV. inaequalispresents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research ofVenturiapathogens. Especially, it will help understanding the evolutionary history ofVenturiaspecies that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.
Women in neotropical science: Gender parity in the 21st century and prospects for a post-war Colombia
Authors: López-Aguirre Camilo
Published: November 2018

An increasing amount of research has focused on studying the drivers shaping demographics in science. As a result, we now have a better idea of the current state of gender disparity in science, which remains widespread worldwide. However, fewer studies and limited data have restricted our understanding of this phenomenon in the Neotropics, a highly important region in terms of cultural and biological diversity. Despite a civil war that lasted more than five decades and produced eight million victims (half of them women), Colombia is the fifth country with the highest scientific production in Latin America and the Caribbean, as well as the second most biodiverse country in the world. In order to evaluate the status of gender parity in science in Colombia throughout the 21st century, data of science demographics was gathered covering the 2000-2017 time period. Percentage of women in science was decomposed by research area, researcher rank level and education level. Gender disparity was also estimated for changes in average age, access to scholarships for postgraduate studies, and number of doctoral graduates. Finally, using logistic function modelling, temporal projections into the future were performed, in order to estimate how long could it take to reach gender parity. Of six research fields, medical and health science is the only one to have reached gender parity (55.99%), although it is also the only one showing a steady decrease in women representation across time. On the other hand, engineering, humanities and natural sciences had the lowest percentages of female representation (19.89%, 30.02%, and 30.21%, respectively). Female researchers were on average younger than male researchers, and they also showed a decreasing presence as they move upward to more senior levels, exemplifying the ‘leaky-pipeline phenomenon’ common in science. More men were observed both as scholarship awardees for doctoral studies, and as doctoral graduates, indicating that obtaining a doctoral degree could be a major limiting factor for women in science. Possible drivers of these results are analysed, suggesting that a combination of lack of research funding, insufficient legal framework, pre-existing biases, and poor protection of women’s rights inhibits female participation in science. Based on logistic function modelling it is estimated that, without any action to change current trends, it could take between 10 (humanities) and 175 (engineering) years to reach gender parity across all research areas.