bluuebunny/crossref_metadata_2025_split huggingface dataset:
A web-based, branching logic questionnaire for the automated classification of migraine
Authors: Kaiser Eric A. , Igdalova Aleksandra , Aguirre Geoffrey K. , Cucchiara Brett 
Published: July 2018

AbstractObjectiveTo identify migraineurs and headache-free individuals with an online questionnaire and automated analysis algorithm.MethodsWe created a branching-logic, web-based questionnaire—the Penn Online Evaluation of Migraine (POEM)—to obtain standardized headache history from a previously studied cohort. Responses were analyzed with an automated algorithm to assign subjects to one of several categories based on ICHD-3 (beta) criteria. Following a pre-registered protocol, this result was compared to prior diagnostic classification by a neurologist following a direct interview.ResultsOf 118 subjects contacted, 90 (76%) completed the questionnaire; of these 31 were headache-free, 29 migraine without aura (MwoA), and 30 migraine with aura (MwA). Mean age was 41 ± 6 years and 76% were female. There were no significant demographic differences between groups. The median time to complete the questionnaire was 2.5 minutes. Sensitivity of the POEM tool was 42%, 59%, and 70%, and specificity was 100%, 84%, and 94% for headache-free, MwoA, and MwA, respectively. Sensitivity and specificity of the POEM tool for migraine overall (with or without aura), was 83% and 90%, respectively.ConclusionsThe POEM web-based questionnaire, and associated analysis routines, identifies headache-free and migraine subjects with good specificity. It may be useful for classifying subjects for large-scale research studies.Trial Registration:https://osf.io/sq9ef
Impact of 10-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya
Authors: Hammitt Laura L. , Etyang Anthony O. , Morpeth Susan C. , Ojal John , Mutuku Alex , Mturi Neema , Moisi Jennifer C. , Adetifa Ifedayo M. , Karani Angela , Akech Donald O. , Otiende Mark , Bwanaali Tahreni , Wafula Jackline , Mataza Christine , Mumbo Edward , Tabu Collins , Knoll Maria Deloria , Bauni Evasius , Marsh Kevin , Williams Thomas N. , Kamau Tatu , Sharif Shahnaaz K. , Levine Orin S. , Scott J. Anthony G. 
Published: July 2018

AbstractBackground10-valent pneumococcal conjugate vaccine (PCV10), delivered at 6, 10 and 14 weeks of age, was introduced in Kenya in January 2011, accompanied by a catch-up campaign in Kilifi County for children <5 years. Coverage with ≥2 PCV10 doses in children 2-11 months was 80% in 2011 and 84% in 2016; coverage with ≥1 dose in children 12-59 months was 66% and 87%, respectively.MethodsClinical and microbiological surveillance for invasive pneumococcal disease (IPD) among admissions of all ages at Kilifi County Hospital was linked to the Kilifi Health and Demographic Surveillance System from 1999-2016. We calculated the incidence rate ratio (IRR) comparing the pre-vaccine and post-vaccine eras, adjusted for confounding, and reported percent reduction in IPD as 1-IRR. Annual cross-sectional surveys of nasopharyngeal carriage were conducted from 2009-2016.FindingsSurveillance identified 667 IPD cases in 3,211,403 person-years of observation. IPD incidence in children <5 years fell sharply in 2011 following PCV10 introduction, and remained low (PCV10-type IPD: 60·8 vs 3·2/100,000 [92% reduction; 95%CI: 78, 97]; overall IPD: 81·6 vs 15·3/100,000 [68% reduction; 95%CI: 40, 83]; 1999-2010 vs 2012-2016). PCV10-type IPD also declined significantly in unvaccinated age groups (<2 months, 5-14 years, ≥15 years), with estimated reductions of 100%, 74%, and 81%, respectively. There was no significant change in the incidence of non-PCV10 type IPD. In children aged <5 years, PCV10-type carriage declined by 74% and non-PCV10-type carriage increased by 71%.InterpretationIntroduction of PCV10 in Kenya resulted in a substantial reduction in PCV10-type IPD in children and adults without significant replacement disease. These findings suggest that routine infant PCV10 immunization programmes with catch-up campaigns will provide substantial direct and indirect protection in low-income settings in tropical Africa.
Modern wolves trace their origin to a late Pleistocene expansion from Beringia
Authors: Loog Liisa , Thalmann Olaf , Sinding Mikkel-Holger S. , Schuenemann Verena J. , Perri Angela , Germonpré Mietje , Bocherens Herve , Witt Kelsey E. , Samaniego Castruita Jose A. , Velasco Marcela S. , Lundstrøm Inge K. C. , Wales Nathan , Sonet Gontran , Frantz Laurent , Schroeder Hannes , Budd Jane , Jimenez Elodie-Laure , Fedorov Sergey , Gasparyan Boris , Kandel Andrew W. , Lázničková-Galetová Martina , Napierala Hannes , Uerpmann Hans-Peter , Nikolskiy Pavel A. , Pavlova Elena Y. , Pitulko Vladimir V. , Herzig Karl-Heinz , Malhi Ripan S. , Willerslev Eske , Hansen Anders J. , Dobney Keith , Gilbert M. Thomas P. , Krause Johannes , Larson Greger , Eriksson Anders , Manica Andrea 
Published: July 2018

ABSTRACTGrey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
Metabolically activated macrophages in mammary adipose tissue link obesity to triple-negative breast cancer
Authors: Tiwari Payal , Blank Ariane , Cui Chang , Schoenfelt Kelly Q. , Zhou Guolin , Xu Yanfei , Shah Ajay M. , Khan Seema A. , Rosner Marsha Rich , Becker Lev 
Published: July 2018

SUMMARYObesity is associated with increased incidence and severity of triple-negative breast cancer (TNBC); however, mechanisms underlying this relationship are incompletely understood. Macrophages, which accumulate in adipose tissue and are activated during obesity, are an attractive mechanistic link. Here, we show that, during obesity, murine and human mammary adipose tissue macrophages adopt a pro-inflammatory, metabolically- activated (MMe) macrophage phenotype that promotes TNBC stem-like markers and functions, including increased tumorsphere growthin vitroand tumor-initiating potentialin vivo. We demonstrate that MMe macrophages release cytokines in an NADPH oxidase 2 (NOX2)-dependent manner that signal through glycoprotein 130 (GP130) on TNBC cells to promote their stem-like properties. Accordingly, deletingNox2in myeloid cells or depleting GP130 in TNBC cells attenuates the ability of obesity to drive TNBC tumor formation. Our studies implicate MMe macrophage accumulation in mammary adipose tissue during obesity as a mechanism for promoting TNBC stemness and tumorigenesis.HIGHLIGHTS⁘Obesity promotes TNBC tumor formation and stemness.⁘Mammary adipose tissue macrophages are metabolically activated (MMe) in obese mice and humans.⁘MMe macrophages in mammary adipose tissue contribute to obesity-induced stemness.⁘MMe macrophages promote TNBC stemness through GP130 signaling.
Bcl6 promotes neurogenic conversion through transcriptional repression of multiple self-renewal-promoting extrinsic pathways
Authors: Bonnefont Jerome , Tiberi Luca , van den Ameele Jelle , Potier Delphine , Gaber Zachary B , Lin Xionghui , Bilheu Angéline , Herpoel Adèle , Velez Bravo Fausto D. , Guillemot François , Aerts Stein , Vanderhaeghen Pierre 
Published: July 2018

SummaryDuring neurogenesis, progenitors switch from self-renewal to differentiation through the interplay of intrinsic and extrinsic cues, but how these are integrated remains poorly understood. Here we combine whole genome transcriptional and epigenetic analyses with in vivo functional studies and show that Bcl6, a transcriptional repressor known to promote neurogenesis, acts as a key driver of the neurogenic transition through direct silencing of a selective repertoire of genes belonging to multiple extrinsic pathways promoting self-renewal, most strikingly the Wnt pathway. At the molecular level, Bcl6 acts through both generic and pathway-specific mechanisms. Our data identify a molecular logic by which a single cell-intrinsic factor ensures robustness of neural cell fate transition by decreasing responsiveness to the extrinsic pathways that favor self-renewal.
Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution
Authors: Chaw Shu-Miaw , Liu Yu-Ching , Wang Han-Yu , Wu Yu-Wei , Ivy Lin Chan-Yi , Wu Chung-Shien , Ke Huei-Mien , Chang Lo-Yu , Hsu Chih-Yao , Yang Hui-Ting , Sudianto Edi , Hsu Ming-Hung , Wu Kun-Pin , Wang Ning-Ni , Leebens-Mack Jim , Tsai Isheng. J. 
Published: July 2018

AbstractWe present reference-quality genome assembly and annotation for the stout camphor tree (SCT;Cinnamomum kanehirae[Laurales, Lauraceae]), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales, and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry relative to monocots. Two whole genome duplication events were inferred within the magnoliid lineage, one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history ofCinnamomum. For example, expansion of terpenoid synthase subfamilies within the Laurales spawned the diversity ofCinnamomummonoterpenes and sesquiterpenes.
The equivocal mean age of parents in a cohort
Authors: Bienvenu François 
Published: July 2018

AbstractThe mean age at childbirth is an important notion in demography, ecology and evolution, where it is used as a measure of generation time. A standard way to quantify it is to compute the mean age of the parents of all offspring produced by a cohort, and the resulting measure is thought to represent the mean age at which a typical parent produces offspring. In this note, I explain why this interpretation is problematic. I also introduce a new measure of the mean age at reproduction and show that it can be very different from the mean age of parents of offspring of a cohort. In particular, the mean age of parents of offspring of a cohort systematically overestimates the mean age at reproduction, and can even be greater than the expected lifespan of parents.
Shared expression of Crassulacean acid metabolism (CAM) genes predates the origin of CAM in the genusYucca
Authors: Heyduk Karolina , Ray Jeremy N. , Ayyampalayam Saaravanaraj , Moledina Nida , Borland Anne , Harding Scott A. , Tsai Chung-Jui , Mack Jim Leebens 
Published: July 2018

Highlight:Although large differences in metabolism exist between C3and CAM species, we find that many CAM genes have shared expression patterns regardless of photosynthetic pathway, suggesting ancestral propensity for CAM.Abstract:Crassulacean acid metabolism (CAM) is a carbon-concentrating mechanism that has evolved numerous times across flowering plants and is thought to be an adaptation to water limited environments. CAM has been investigated from physiological and biochemical perspectives, but little is known about how plants evolve from C3to CAM at the genetic or metabolic level. Here we take a comparative approach in analyzing time-course data of C3, CAM, and C3+CAM intermediateYucca(Asparagaceae) species. RNA samples were collected over a 24-hour period from both well-watered and drought-stressed plants and were clustered based on time-dependent expression patterns. Metabolomic data reveals differences in carbohydrate metabolism and antioxidant response between the CAM and C3species, suggesting changes to metabolic pathways are important for CAM evolution and function. However, all three species share expression profiles of canonical CAM pathway genes, regardless of photosynthetic pathway. Despite differences in transcript and metabolite profiles between the C3and CAM species, shared time-structured expression of CAM genes in both CAM and C3Yuccaspecies suggests ancestral expression patterns required for CAM may have predated its origin inYucca.
Sex makes them sleepy: host reproductive status induces diapause in a parasitoid population experiencing harsh winters
Authors: Tougeron K. , Brodeur J. , van Baaren J. , Renault D. , Le Lann C. 
Published: July 2018

AbstractWhen organisms coevolve, any change in one species can induce phenotypic changes in traits and ecology of the other species. The role such interactions play in ecosystems is central, but their mechanistic bases remain underexplored. Upper trophic level species have to synchronize their life-cycle to both abiotic conditions and to lower trophic level species’ phenology and phenotypic variations. We tested the effect of host seasonal strategy on parasitoid diapause induction by using a holocyclic clone of the pea aphidAcyrthosiphon pisumproducing asexual and sexual morphs that are viviparous females (i.e. laying embryos) and oviparous females (laying eggs), respectively, the latter being only present at the end of the growing season.Aphidius erviparasitoids from populations of contrasted climatic origin (harsh vs. mild winter areas) were allowed to parasitize each morph in a split-brood design and developing parasitoids were next reared under either fall-like or summer-like temperature-photoperiod conditions. We next examined aspects of the host physiological state by comparing the relative proportion of forty-seven metabolites and lipid reserves in both morphs produced under the same conditions. We found that oviparous morphs are cuesper sefor diapause induction; parasitoids entered diapause at higher levels when developing in oviparous hosts (19.4 ± 3.0%) than in viviparous ones (3.6 ± 1.3%), under summer-like conditions (i.e., when oviparous aphids appear in the fields). This pattern was only observed in parasitoids from the harsh winter area since low diapause levels were observed in the other population, suggesting local adaptations to overwintering cues. Metabolomics analyses show parasitoids’ response to be mainly influenced by the host’s physiology, with higher proportion of polyols and sugars, and more fat reserves being found in oviparous morphs. Host quality thus varies across the seasons and represents one of the multiple environmental parameters affecting parasitoid diapause. Our results underline strong coevolutionary processes between hosts and parasitoids in their area of origin, likely leading to phenological synchronization, and we point out the importance of such bottom-up effects for trait expression, and for the provision of ecosystem services such as biological control in the context of climate change.
MICU1 modulates MCU ion selectivity and tolerance to manganese stress
Authors: Wettmarshausen Jennifer , Goh Valerie , Tripathi Utkarsh , Leimpek Anja , Cheng Yiming , Pittis Alexandros A. , Gabaldón Toni , Mokranjac Dejana , Perocchi Fabiana 
Published: July 2018

SUMMARYThe mitochondrial calcium uniporter is a highly selective ion channel composed of species-and tissue-specific structural and regulatory subunits. However, the contribution of each component to uniporter-mediated activity still remains unclear. Here, we employ an evolutionary and synthetic biology approach to investigate the functional inter-dependence between the pore-forming subunit MCU and the EF-hand protein MICU1. Using phylogenetic profiling and genetic complementation analyses, we show that MCU and MICU1 constitute the minimal eukaryotic unit of the uniporter, pointing towards a strong selective pressure behind their co-occurrence. Heterologous reconstitution of MCU-mediated and MICU1-gated mitochondrial calcium entryin vivoin yeast cells demonstrates that MICU1per seis essential to protect yeast from MCU-dependent manganese cytotoxicity. Accordingly, MICU1 deletion significantly sensitizes human HEK-293 cells to manganese-induced stress. Our study identifies a critical role of MICU1 in the regulation of MCU ion selectivity, with potential implications for patients with MICU1 deficiency.
The ecological cocktail party: Measuring brain activity during an auditory oddball task with background noise
Authors: Scanlon Joanna E. M. , Cormier Danielle L. , Townsend Kimberley A. , Kuziek Jonathan W.P. , Mathewson Kyle E. 
Published: July 2018

AbstractMost experiments using EEG recordings take place in highly isolated and restricted environments, limiting their applicability to real-life scenarios. New technologies for mobile EEG are changing this by allowing EEG recording to take place outside of the laboratory. However, before results from experiments performed outside the laboratory can be fully understood, the effects of ecological stimuli on brain activity during cognitive tasks must be examined. In this experiment, participants performed an auditory oddball task while also listening to concurrent background noises of silence, white noise and outdoor ecological sounds, as well as a condition in which the tones themselves were at a low volume. We found a significantly increased N1 and decreased P2 when participants performed the task with outdoor sounds and white noise in the background, with the largest differences in the outdoor sound condition. This modulation in the N1 and P2 replicates what we have previously found outside while people ride bicycles (Scanlon et al., 2017b). No behavioural differences were found in response to the target tones. We interpret these modulations in early ERPs as indicative of sensory filtering of background sounds, and that ecologically valid sounds require more filtering than synthetic sounds. Our results reveal that much of what we understand about the brain will need to be updated as we step outside the lab.
The splicing factor U2AF1 contributes to cancer progression through a non-canonical role in translation regulation
Authors: Palangat Murali , Anastasakis Dimitrios , Liang Fei , Lindblad Katherine E. , Bradley Robert , Hourigan Christopher S. , Hafner Markus , Larson Daniel R. 
Published: July 2018

AbstractSomatic mutations in the genes encoding components of the spliceosome occur frequently in human neoplasms, including myeloid dysplasias and leukemias and less often in solid tumors. One of the affected factors, U2AF1, is involved in splice site selection, and the most common change, S34F, alters a conserved nucleic acid binding domain, recognition of the 3’-splice site, and alternative splicing of many mRNAs. However, the role that this mutation plays in oncogenesis is still unknown. Here, we have uncovered a non-canonical function of U2AF1, showing that it binds mature mRNA in the cytoplasm and negatively regulates mRNA translation. This splicing-independent role of U2AF1 is altered by the S34F mutation, and polysomal profiling indicates the mutation affects translation of hundreds of mRNA. One functional consequence is increased synthesis of the secreted chemokine interleukin 8 which contributes to metastasis, inflammation, and cancer progression in mice and humans.
Entomophthovirus: An insect-derived iflavirus that infects a behavior manipulating fungal pathogen of dipterans
Authors: Coyle Maxwell C. , Elya Carolyn N. , Bronski Michael , Eisen Michael B. 
Published: July 2018

AbstractWe discovered a virus infecting Entomophthora muscae, a behavior-manipulating fungal pathogen of dipterans. The virus, which we name Entomophthovirus, is a capsid-forming, positive-strand RNA virus in the viral family iflaviridae, whose known members almost exclusively infect insects. We show that the virus RNA is expressed at high levels in fungal cells in vitro and during in vivo infections of Drosophila melanogaster, and that virus particles are present in E. muscae. Two close relatives of the virus had been previously described as insect viruses based on the presence of viral genomes in transcriptomes assembled from RNA extracted from wild dipterans. By analyzing sequencing data from these earlier reports, we show that both dipteran samples were co-infected with E. muscae. We also find the virus in RNA sequencing data from samples of two other species of dipterans, Musca domestica and Delia radicum, known to be infected with E. muscae. These data establish that Entomophthovirus is widely, and seemingly obligately, associated with E. muscae. As other members of the iflaviridae cause behavioral changes in insects, we speculate on the possibility that Entomophthovirus plays a role in E. muscae involved host manipulation.
A novel generic dictionary-based denoising method for improving noisy and densely packed nuclei segmentation in 3D time-lapse fluorescence microscopy images
Authors: Nasser Lamees , Boudier Thomas 
Published: July 2018

ABSTRACTTime-lapse fluorescence microscopy is an essential technique for quantifying various characteristics of cellular processes,i.e. cell survival, migration, and differentiation. To perform high-throughput quantification of cellular processes, nuclei segmentation and tracking should be performed in an automated manner. Nevertheless, nuclei segmentation and tracking are challenging tasks due to embedded noise, intensity inhomogeneity, shape variation as well as a weak boundary of nuclei. Although several nuclei segmentation approaches have been reported in the literature, dealing with embedded noise remains the most challenging part of any segmentation algorithm. We propose a novel denoising algorithms, based on sparse coding, that can both enhance very faint and noisy nuclei but simultaneously detect nuclei position accurately. Furthermore our method is based on a limited number of parameters,with only one being critical, which is the approximate size of the objects of interest. We also show that our denoising method coupled with classical segmentation method works properly in the context of the most challenging cases. To evaluate the performance of the proposed method, we tested our method on two datasets from the cell tracking challenge. Across all datasets, the proposed method achieved satisfactory results with 96.96% recall forC.elegansdataset. Besides, inDrosophiladataset, our method achieved very high recall (99.3%).