bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing short and long batteries to assess deficits and their neural bases in stroke aphasia
Authors: Halai Ajay D. , De Dios Perez Blanca , Stefaniak James D. , Lambon Ralph Matthew A. 
Published: November 2020

AbstractMultiple language assessments are necessary for diagnosing, characterising and quantifying the multifaceted deficits observed in many patients’ post-stroke. Current language batteries, however, tend to be an imperfect trade-off between time and sensitivity of assessment. There have hitherto been two main types of battery. Extensive batteries provide thorough information but are impractically long for application in clinical settings or large-scale research studies. Clinically-targeted batteries tend to provide superficial information about a large number of language skills in a relatively short period of time by reducing the depth of each test but, consequently, can struggle to identify mild deficits, qualify the level of each impairment or reveal the underlying component structure. In the current study, we compared these batteries across a large group of individuals with chronic stroke aphasia to determine their utility. In addition, we developed a data-driven reduced version of an extensive battery that maintained sensitivity to mild impairment, ability to grade deficits and the component structure. The underlying structure of these three language batteries (extensive, shallow and data-reduced) was analysed using cross-validation analysis and principal component analysis. This revealed a four-factor solution for the extensive and data-reduced batteries, identifying phonology, semantic skills, fluency and executive function in contrast to a two-factor solution using the shallow battery (phonological/language severity and cognitive severity). Lesion symptom mapping using participants’ factor scores identified convergent neural structures based on existing language models for phonology (superior temporal gyrus), semantics (inferior temporal gyrus), speech fluency (precentral gyrus) and executive function (lateral occipitotemporal cortex) based on the extensive and data-reduced batteries. The two components in the shallow battery converged with the phonology and executive function clusters. In addition, we show that multivariate prediction models could be utilised to predict the component scores using neural data, however not for every component score within every test battery. Overall, the data-reduced battery appears to be an effective way to save assessment time yet retain the underlying structure of language and cognitive deficits observed in post stroke aphasia.
A highly efficient gene disruption strategy reveals lipid co-regulatory networks
Authors: Harayama Takeshi , Hashidate-Yoshida Tomomi , Fleuriot Lucile , Aguilera-Romero Auxiliadora , Hamano Fumie , Ri Keiken , Morimoto Ryo , Debayle Delphine , Shimizu Takao , Riezman Howard 
Published: November 2020

SUMMARYGene disruption has been dramatically facilitated by genome editing tools. Despite improvements in gene disruption rates in cultured cells, clone isolation remains routinely performed to obtain mutants, potentially leading to artifacts due to clonal variation in cellular phenotypes. Here we report GENF, a highly efficient strategy to disrupt genes without isolating clones, which can be multiplexed. Using it, we obtained reliable lipidomics datasets from mutant cells without being affected by variances related to clone isolation. Through this, we found that an enzyme involved in congenital generalized lipodystrophy regulates glycerophospholipids with specific acyl-chains. We also demonstrate the possibility to dissect complex lipid co-regulatory mechanisms, explaining cell adaptations to altered lipid metabolism. With its simplicity and the avoidance of cloning-related artifacts, GENF is likely to contribute to many cell biology studies, especially those involving -omics approaches.
Missing pieces in the full annual cycle of fish ecology: a systematic review of the phenology of freshwater fish research
Authors: Brady Megan E. , Chione Andrew M. , Armstrong Jonathan B. 
Published: November 2020

AbstractIn recent decades, fish ecologists have become increasingly aware of the need for spatially comprehensive sampling. However, a corresponding reflection on the temporal aspects of research has been lacking. We quantified the seasonal timing and extent of freshwater fish research. Since reviewing all prior work was not feasible, we considered two different subsets. First, we compiled the last 30 years of ecological research on juvenile Pacific salmon and trout (Oncorhynchusspp.) (n = 371 studies). In addition to the aggregate, we compared groups classified by subject matter. Next, to evaluate whether riverscape ecology has embraced space at the expense of time, we compiled research across taxa in which fish were enumerated in a spatially continuous fashion (n = 46). We found that ecologicalOncorhynchusspp. research was biased towards summer (40% occurred during June-August) and the month of June in particular, at the expense of winter work (only 13% occurred during December-February). Riverscape studies were also biased toward summer (47% of studies) and against winter (11%). It was less common for studies to encompass multiple seasons (43% of ecologicalOncorhynchusspp. studies and 54% of riverscape studies) and most were shorter than 4 months (73% of ecologicalOncorhynchusspp. studies and 81% of riverscape studies). These temporal biases may cause researchers to overemphasize ecological phenomena observed during summer and limit our ability to recognize seasonal interactions such as carry-over effects or compensatory responses. Full year and winter studies likely hold valuable insights for conservation and management.
Application of Microencapsulation Technology in Mushroom Powder Cake Processing
Authors: Zifei Liu , Hongyan Ye , Wei Yue , Li Ning 
Published: November 2020

AbstractIn this study,Lentinus edodes(or mushroom) powder and carrot juice were used as raw materials to prepare a new type of nutritious cakes. Microencapsulation was applied in embedding vitamin C to prevent the loss of this vitamin during baking at high temperatures. The most suitable addition amount of each materials was optimized via single-factor test and response surface analysis. The optimal microencapsulation of shiitake mushroom powder with carrot juice required 10 g of mushroom powder, 35 g of soft sugar, 50 mL of carrot juice and 160 g of egg white. The cake prepared herein was rich in nutrient and exuded a unique flavor. This cake was prepared via modern processing technologies and efficient detection techniques. Microencapsulation not only improves the nutritional value of traditional flour products but also expands the scope of research on food processing technologies.Practical applicationsLentinus edodesis a nutritious food with low fat content and rich in polysaccharides and vitamins. Consumption of this mushroom improves immunity, lowers blood pressure, and prevents the development of various types of cancer. GroundL. edodespowder is also called mushroom powder, which has the same nutrient composition and efficacy asL.entinus edodes. Carrots produce a fresh aroma, and the large amounts of β -carotene in carrots improve the nutritional value of carrot-based food and also exert beneficial effects, such as preventing xerophthalmia, night blindness, and oral ulcer. A new cake made of carrot juice and mushroom powder can effectively improve the nutritional and economic values of carrot and mushroom powder. However, vitamin C easily loses its function at high temperatures. In this study, vitamin C was microencapsulated to reduce its outflow. The purpose of this study was to expand the applications of microencapsulation technology, provide a scientific basis for the production of nutritious functional foods, and offer new research ideas for the development of new cakes.
Temporal Requirements of SKN-1/NRF as a Regulator of Lifespan and Proteostasis inCaenorhabditis elegans
Authors: Grushko Danielle , Levine Amir , Boocholez Hana , Cohen Ehud 
Published: November 2020

AbstractLowering the activity of the Insulin/IGF-1 Signaling (IIS) cascade results in elevated stress resistance, enhanced protein homeostasis (proteostasis) and extended lifespan of worms, flies and mice. In the nematodeCaenorhabditis elegans(C. elegans), the longevity phenotype that stems from IIS reduction is entirely dependent upon the activities of a subset of transcription factors including the Forkhead factor DAF-16/FOXO (DAF-16), Heat Shock Factor-1 (HSF-1), SKiNhead/Nrf (SKN-1) and ParaQuat Methylviologen responsive (PQM-1). While DAF-16 determines lifespan exclusively during early adulthood and governs proteostasis in early adulthood and midlife, HSF-1 executes these functions foremost during development. Despite the central roles of SKN-1 as a regulator of lifespan and proteostasis, the temporal requirements of this transcription factor were unknown. Here we employed conditional knockdown techniques and discovered that inC. elegans, SKN-1 is primarily important for longevity and proteostasis during late larval development through early adulthood. Our findings indicate that events that occur during late larval developmental through early adulthood affect lifespan and proteostasis and suggest that subsequent to HSF-1, SKN-1 sets the conditions, partially overlapping temporally with DAF-16, that enable IIS reduction to promote longevity and proteostasis. Our findings raise the intriguing possibility that HSF-1, SKN-1 and DAF-16 function in a coordinated and sequential manner to promote healthy aging.
EoRNA, a barley gene and transcript abundance database
Authors: Milne Linda , Bayer Micha , Rapazote-Flores Paulo , Mayer Claus-Dieter , Waugh Robbie , Simpson Craig G 
Published: November 2020

AbstractA high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EoRNA* – Expression of RNA) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EoRNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley
The ESCRT-III machinery participates in the production of extracellular vesicles and protein export duringPlasmodium falciparuminfection
Authors: Avalos-Padilla Yunuen , Georgiev Vasil N. , Lantero Elena , Pujals Silvia , Verhoef René , Borgheti-Cardoso Livia N. , Albertazzi Lorenzo , Dimova Rumiana , Fernàndez-Busquets Xavier 
Published: November 2020

AbstractInfection withPlasmodium falciparumenhances extracellular vesicles (EVs) production in parasitized red blood cells (pRBC), an important mechanism for parasite-to-parasite communication during the asexual intraerythrocytic life cycle. Theendosomalsortingcomplexrequired fortransport (ESCRT), and in particular the ESCRT-III sub-complex, participates in the formation of EVs in higher eukaryotes. However, RBCs have lost the majority of their organelles through the maturation process, including an important reduction in their vesicular network. Therefore, the mechanism of EV production inP. falciparum-infected RBCs remains to be elucidated. Here we demonstrate thatP. falciparumpossesses a functional ESCRT-III machinery that is activated by an alternative recruitment pathway involving the action of PfBro1 and PfVps32/PfVps60 proteins. Additionally, multivesicular bodies formation and membrane shedding, both reported mechanisms of EVs production, were reconstituted in the membrane model of giant unilamellar vesicles using the purified recombinant proteins. Moreover, the presence of PfVps32, PfVps60 and PfBro1 in EVs purified from a pRBC culture was confirmed by super-resolution microscopy. In accordance, disruption of thePfvps60gene led to a reduction in the number of the produced EVs in the KO strain when compared with the parental 3D7 strain. Overall, our results increase the knowledge on the underlying molecular mechanisms during malaria pathogenesis and demonstrate that ESCRT-IIIP. falciparumproteins participate in EVs production.
Separation and enrichment of sodium-motile bacteria using cost-effective microfluidics
Authors: Gurung Jyoti P , Kashani Moein Navvab , Agarwal Sanaz , Peralta Gonzalo , Gel Murat , Baker Matthew AB 
Published: November 2020

ABSTRACTMany motile bacteria are propelled by the rotation of flagellar filaments. This rotation is driven by a membrane protein known as the stator-complex, which drives the rotor of the bacterial flagellar motor. Torque generation is powered in most cases by proton transit through membrane protein complexes known as stators, with the next most common ionic power source being sodium. Sodium-powered stators can be studied through the use synthetic chimeric stators that combine parts of sodium- and proton-powered stator proteins. The most well studied example is the use of the sodium powered PomA-PotB chimeric stator unit in the naturally proton-poweredE. coli. Here we designed a fluidics system at low cost for rapid prototyping to separate motile and non-motile populations of bacteria while varying the ionic composition of the media and thus the sodium-motive-force available to drive this chimeric flagellar motor. We measured separation efficiencies at varying ionic concentrations and confirmed using fluorescence that our device delivered eight-fold enrichment of the motile proportion of a mixed population. Furthermore, our results showed that we could select bacteria from reservoirs where sodium was not initially present. Overall, this technique can be used to implement selection of highly-motile fractions from mixed liquid cultures, with applications in directed evolution to investigate the adaptation of motility in bacterial ecosystems.
Diverse natural variants suppress mutations in hundreds of essential genes
Authors: Parts Leopold , Batté Amandine , Lopes Maykel , Yuen Michael W. , Laver Meredith , San Luis Bryan-Joseph , Yue Jia-Xing , Pons Carles , Eray Elise , Aloy Patrick , Liti Gianni , van Leeuwen Jolanda 
Published: November 2020

AbstractThe consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, but lead to lethality in another. The extent to which mutant phenotypes are malleable, the complexity of the architecture of modifiers, and the identities of causal genes and pathways remain largely unknown. Here, we measure the fitness effects of ~1,500 temperature sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds, and map the modifiers for 19 combinations. Altogether, fitness defects for 183 of the 530 tested genes (35%) could be suppressed by standing genetic variation in at least one wild strain. Suppression was generally driven by gain-of-function of a single, strong modifier gene. The validated causes included both variants in protein interaction partners or pathway members suppressing specific genes, as well as general modifiers altering the effect of many temperature sensitive alleles. The emerging frequency of suppression and range of possible suppression mechanisms suggest that a substantial fraction of monogenic diseases could be repressed by modulating other gene products.
Copy number signatures predict chromothripsis and associate with poor clinical outcomes in patients with newly diagnosed multiple myeloma
Authors: Maclachlan Kylee H , Rustad Even H , Derkach Andriy , Zheng-Lin Binbin , Yellapantula Venkata , Diamond Benjamin , Hultcrantz Malin , Ziccheddu Bachisio , Boyle Eileen , Blaney Patrick , Bolli Niccolò , Zhang Yanming , Dogan Ahmet , Lesokhin Alexander , Morgan Gareth , Landgren Ola , Maura Francesco 
Published: November 2020

AbstractChromothripsis is detectable in 20-30% of newly diagnosed multiple myeloma (NDMM) patients and is emerging as a new independent adverse prognostic factor. In this study, we interrogate 752 NDMM patients using whole genome sequencing (WGS) to study the relationship of copy number (CN) signatures to chromothripsis and show they are highly associated. CN signatures are highly predictive of the presence of chromothripsis (AUC=0.90) and can be used to identify its adverse prognostic impact. The ability of CN signatures to predict the presence of chromothripsis was confirmed in a validation series of WGS comprised of 235 hematological cancers (AUC=0.97) and an independent series of 34 NDMM (AUC=0.87). We show that CN signatures can also be derived from whole exome data (WES) and using 677 cases from the same series of NDMM, we were able to predict both the presence of chromothripsis (AUC=0.82) and its adverse prognostic impact. CN signatures constitute a flexible tool to identify the presence of chromothripsis and is applicable to WES and WGS data.
Disease specific alterations in the olfactory mucosa of patients with Alzheimer’s disease
Authors: Lampinen Riikka , Fazaludeen Mohammad Feroze , Avesani Simone , Örd Tiit , Penttilä Elina , Lehtola Juha-Matti , Saari Toni , Hannonen Sanna , Saveleva Liudmila , Kaartinen Emma , Acosta Francisco Fernandez , Cruz-Haces Marcela , Löppönen Heikki , Mackay-Sim Alan , Malm Tarja , Kaikkonen Minna U , Koivisto Anne M , White Anthony R , Giugno Rosalba , Chew Sweelin , Kanninen Katja M 
Published: November 2020

ABSTRACTOlfactory dysfunction manifests early in several neurodegenerative disorders. Olfaction is orchestrated by olfactory mucosal cells located in the upper nasal cavity. However, it is unclear how this tissue reflects key neurodegenerative features in Alzheimer’s disease. Here we report that Alzheimer’s disease olfactory mucosal cells obtained from live individuals secrete toxic amyloid-beta. We detail cell-type-specific gene expression patterns, unveiling 147 differentially expressed disease-associated genes compared to the cognitively healthy controls, and 5 distinct populations in globose basal cell -, myofibroblast-, and fibroblast/ stromal – like cellsin vitro. Overall, coordinated alteration of RNA and protein metabolism, inflammatory processes and signal transduction were observed in multiple cell populations, suggesting a key role in pathophysiology. Our results demonstrate the potential of olfactory cell cultures in modelling Alzheimer’s disease advocate their use for diagnostic purposes. Moreover, for the first time we provide single cell data on olfactory mucosa in Alzheimer’s disease for investigating molecular and cellular mechanisms associated with the disease.
Initial ciliary assembly inChlamydomonasrequires Arp2/3 complex-dependent endocytosis
Authors: Bigge Brae M , Rosenthal Nicholas E , Avasthi Prachee 
Published: November 2020

ABSTRACTCiliary assembly, trafficking, and regulation are dependent on microtubules, but the mechanisms of ciliary assembly also require the actin cytoskeleton. Here, we dissect subcellular roles of actin in ciliogenesis by focusing on actin networks nucleated by the Arp2/3 complex in the powerful ciliary model,Chlamydomonas. We find the Arp2/3 complex is required for the initial stages of ciliary assembly when protein and membrane are in high demand but cannot yet be supplied from the Golgi complex. We provide evidence for Arp2/3 complex-dependent endocytosis of ciliary proteins, an increase in endocytic activity upon induction of ciliary growth, and relocalization of plasma membrane proteins to newly formed cilia. Our data support a new model of ciliary protein and membrane trafficking during early ciliogenesis whereby proteins previously targeted to the plasma membrane are reclaimed by Arp2/3 complex-dependent endocytosis for initial ciliary assembly.SUMMARYUsing the ciliary model systemChlamydomonas, we find Arp2/3 complex-mediated endocytosis is needed to reclaim cell body plasma membrane for early ciliary assembly.
Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin
Authors: Nedoluzhko Artem , Sharko Fedor , Tsygankova Svetlana , Boulygina Eugenia , Ibragimova Amina , Teslyuk Anton , Galindo-Villegas Jorge , Rastorguev Sergey 
Published: November 2020

AbstractInterspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples ofG. aculeatusandP. pungitiusand subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.
QuantifyPolarity, a new tool-kit for measuring planar polarized protein distributions and cell properties in developing tissues
Authors: Tan Su Ee , Tan Weijie , Fisher Katherine H. , Strutt David 
Published: November 2020

SummaryThe coordination of cells or structures within the plane of a tissue is known as planar polarization. It is often governed by the asymmetric distribution of planar polarity proteins within cells. A number of quantitative methods have been developed to provide a readout of planar polarization of protein distributions. However, the quantification of planar polarization can be affected by different cell geometries. Hence, we developed a novel planar polarity quantification method based on Principal Component Analysis (PCA) that is shape insensitive. Here, we compare this method with other state-of-the-art methods on simulated models and biological datasets. We found that the PCA method performs robustly in quantifying planar polarity independently of variation in cell geometry. Furthermore, we designed a user-friendly graphical user interface called QuantifyPolarity, equipped with three different methods for automated quantification of polarity. QuantifyPolarity also provides image analysis tools to quantify cell morphology and packing geometry, allowing the relationship of these characteristics to planar polarization to be investigated. This all-in-one tool enables experimentalists with no prior computational expertise to perform high-throughput cell polarity and shape analysis automatically and efficiently.