bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis for the development of cell-type specific labeling to study olfactory circuits
Authors: Koldaeva Anzhelika , Zhang Cary , Huang Yu-Pei , Reinert Janine , Mizuno Seiya , Sugiyama Fumihiro , Takahashi Satoru , Soliman Taha , Matsunami Hiroaki , Fukunaga Izumi 
Published: December 2020

AbstractIn each sensory system of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioural repertoires. These often correspond to different cell types at some stage in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral and tufted cells (MCs and TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, little is known how these two types of projection neurons differ at the mRNA level. Here, we sought to identify genes that are differentially expressed between MCs and TCs, with an ultimate goal to generate a cell-type specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018). Despite many genes showing differential expressions, we identified only a few that were abundantly and consistently expressed only in MCs. After further validating these putative markers usingin-situhybridization, two genes, namelyPkibandLbdh2, remained as promising candidates. Using CRISPR/Cas9-mediated gene editing, we generated Cre-driver lines and analysed the resulting recombination patterns. This analysis indicated that our new inducible Cre-driver line,Lbhd2-CreERT2, can be used to genetically label MCs in a tamoxifen dose-dependent manner, as assessed by soma locations, projection patterns and sensory-evoked responses. Hence this line is a promising tool for future investigations of cell-type specific contributions to olfactory processing and demonstrates the power of publicly accessible data in accelerating science.
The Bardet-Biedl Syndrome complex component BBS1 regulates proteasome-dependent F-actin clearance from the centrosome to enable its translocation to the T cell immune synapse
Authors: Cassioli Chiara , Onnis Anna , Finetti Francesca , Capitani Nagaja , Compeer Ewoud B , Dustin Micheal L , Baldari Cosima T 
Published: December 2020

ABSTRACTComponents of the intraflagellar transport (IFT) system that regulates the assembly of the primary cilium are exploited by the non-ciliated T cell to orchestrate polarized endosome recycling to sustain signaling during immune synapse formation. Here we have investigated the potential role of BBS1, an essential core component of the Bardet-Biedl syndrome complex that cooperates with the IFT system in ciliary protein trafficking, in the assembly of the T cell synapse. We show that BBS1 allows for centrosome polarization towards the immune synapse by promoting its untethering from the nuclear envelope. This function is achieved through the clearance of centrosomal F-actin and its positive regulator WASH, a process that we demonstrate to be dependent on the proteasome. We show that BBS1 regulates this process by coupling the 19S proteasome regulatory subunit to the microtubule motor dynein for its transport to the centrosome. Our data identify the ciliopathy-related protein BBS1 as a new player in T cell synapse assembly that acts upstream of the IFT system to set the stage for polarized vesicular trafficking and sustained signaling.
Automatic generation of ground truth data for the evaluation of clonal grouping methods in B-cell populations
Authors: Abdollahi Nika , de Septenville Anne , Davi Frédéric , Bernardes Juliana S. 
Published: December 2020

MotivationThe adaptive B-cell response is driven by the expansion, somatic hypermutation, and selection of B-cell clones. Their number, size and sequence diversity are essential characteristics of B-cell populations. Identifying clones in B-cell populations is central to several repertoire studies such as statistical analysis, repertoire comparisons, and clonal tracking. Several clonal grouping methods have been developed to group sequences from B-cell immune repertoires. Such methods have been principally evaluated on simulated benchmarks since experimental data containing clonally related sequences can be difficult to obtain. However, experimental data might contains multiple sources of sequence variability hampering their artificial reproduction. Therefore, the generation of high precision ground truth data that preserves real repertoire distributions is necessary to accurately evaluate clonal grouping methods.ResultsWe proposed a novel methodology to generate ground truth data sets from real repertoires. Our procedure requires V(D)J annotations to obtain the initial clones, and iteratively apply an optimisation step that moves sequences among clones to increase their cohesion and separation. We first showed that our method was able to identify clonally-related sequences in simulated repertoires with higher mutation rates, accurately. Next, we demonstrated how real benchmarks (generated by our method) constitute a challenge for clonal grouping methods, when comparing the performance of a widely used clonal grouping algorithm on several generated benchmarks. Our method can be used to generate a high number of benchmarks and contribute to construct more accurate clonal grouping tools.Availability and implementationThe source code and generated data sets are freely available atgithub.com/NikaAb/BCR_GTG
Chromosome-level genome assembly of the common chaffinch (Aves:Fringilla coelebs): a valuable resource for evolutionary biology
Authors: Recuerda María , Vizueta Joel , Cuevas-Caballé Cristian , Blanco Guillermo , Rozas Julio , Milá Borja 
Published: December 2020

AbstractThe common chaffinch,Fringilla coelebs,is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87 Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian dataset. Around 7.8 % of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian and vertebrate evolution.
Inferring system-level brain communication through multi-scale neural activity
Authors: Chang Yin-Jui , Chen Yuan-I , Yeh Hsin-Chih , Carmena Jose M. , Santacruz Samantha R. 
Published: December 2020

AbstractFundamental principles underlying computation in multi-scale brain networks illustrate how multiple brain areas and their coordinated activity give rise to complex cognitive functions. Whereas the population brain activity has been studied in the micro-to meso-scale in building the connections between the dynamical patterns and the behaviors, such studies were often done at a single length scale and lacked an explanatory theory that identifies the neuronal origin across multiple scales. Here we introduce the NeuroBondGraph Network, a dynamical system incorporating both biological-inspired components and deep learning techniques to capture cross-scale dynamics that can infer and map the neural data from multiple scales. We demonstrated our model is not only 3.5 times more accurate than the popular sphere head model but also able to predict synchronous neural activity and extract correlated low-dimensional latent dynamics. We also showed that we can extend our methods to robustly predict held-out data across several weeks. The extracted effective connectivity agreed with the neuroanatomical hierarchy of motor control. Accordingly, the NeuroBondGraph Network opens the door to revealing comprehensive understanding of the brain computation, where network mechanisms of multi-scale communications are critical.
Comparative Analysis of Embryo Proper and Suspensor Transcriptomes in Plant Embryos With Different Morphologies
Authors: Chen Min , Lin Jer-Young , Wu Xiaomeng , Apuya Nestor R. , Henry Kelli F. , Le Brandon H. , Bui Anhthu Q. , Pelletier Julie M. , Cokus Shawn , Pellegrini Matteo , Harada John J. , Goldberg Robert B. 
Published: December 2020

AbstractAn important question is what genes govern the differentiation of plant embryos into suspensor and embryo-proper regions following fertilization and division of the zygote. We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region. We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones, such as gibberellic acid, and other metabolites are up-regulated in giant Scarlet Runner Bean and Common Bean suspensors. Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well – strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper. By contrast, genes controlling transcriptional regulation, development, and cell division are up-regulated primarily within the embryo proper. Transcriptomes from less specialized soybean andArabidopsissuspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated. Genes active in the embryo proper, however, are functionally similar to those active in Scarlet Runner Bean and Common Bean embryo proper regions. We uncovered a set of suspensor- and embryo-proper-specific transcription factors (TFs) that are shared by all embryos irrespective of morphology, suggesting that they are involved in early differentiation processes common to all plants. ChIP-Seq experiments with Scarlet Runner Bean and soybean WOX9, an up-regulated suspensor TF, gained entry into a regulatory network important for suspensor development irrespective of morphology.SignificanceHow plant embryos are differentiated into embryo proper and suspensor regions following fertilization is a major unanswered question. The suspensor is unique because it can vary in morphology in different plant species. We hypothesized that regulatory genes controlling the specification of embryo proper and suspensor regions should be shared by all plants irrespective of embryo morphology. We compared embryo proper and suspensor transcriptomes of plants with distinct suspensor morphologies. Scarlet Runner Bean and Common Bean have highly specialized giant suspensor regions, whereas soybean andArabidopsissuspensors are smaller and less specialized. We uncovered a small set of embryo-proper- and suspensor-specific transcription factors shared by all embryos irrespective of morphology, suggesting that they play an important role in early embryo differentiation.
Suppressing the morning cortisol rise after memory reactivation at 4 a.m. enhances episodic memory reconsolidation in humans
Authors: Antypa Despina , Perrault Aurore A. , Vuilleumier Patrik , Schwartz Sophie , Rimmele Ulrike 
Published: December 2020

AbstractEvidence from animal and human research shows that established memories can undergo changes after reactivation through a process called reconsolidation. Alterations of the level of the stress hormone cortisol may be one way of manipulating reconsolidation. Here, in a double-blind, within-subject design, we reactivated a 3-day-old memory at 3:55 a.m., immediately followed by oral administration of metyrapone vs. placebo, to examine whether metyrapone-induced suppression of the morning cortisol rise may influence reconsolidation processes during and after early morning sleep. Crucially, reactivation followed by cortisol suppression vs. placebo resulted in enhanced memory for the reactivated episode (tested four days after reactivation). This enhancement after cortisol suppression was specific for the reactivated episode vs. a non-reactivated episode. These findings suggest that when reactivation of memories is immediately followed by suppression of cortisol levels during early morning sleep, reconsolidation processes change in a way that leads to the strengthening of episodic memory traces.
Enhancing daily light exposure increases the antibody response to influenza vaccination in patients with dementia
Authors: Münch Mirjam , Goldbach Rolf , Zumstein Naomi , Vonmoos Petra , Scartezzini Jean-Louis , Wirz-Justice Anna , Cajochen Christian 
Published: December 2020

AbstractEnhancing lighting conditions in institutions for individuals with dementia improves their sleep, circadian rhythms and well-being. Here, we tested whether a greater long-term daily light exposure supports the immune response to the annual influenza vaccination. Eighty older institutionalised patients suffering from dementia (54 women and 26 men) continuously wore an activity tracker for 8 weeks to assess individual light exposure and rest-activity cycles. The patients’ immune response was analysed from two blood samples taken before and 4 - 5 weeks after the annual influenza vaccination. Individual antibody concentrations to three influenza virus strains (H3N2, H1N1, IB) were quantified via hemagglutination inhibition assays. By quantifying individual light exposure profiles (including daylight), we classified the patients into a low and a high light exposure group based on a median illuminance of 392.6 lux. The two light exposure groups did not differ in cognitive impairment severity, age or gender distribution. However, patients in the high light exposure group showed a significantly greater circadian rest-activity amplitude (i.e., more daytime activity and less nighttime activity) along with a significantly greater antibody titer increase to the H3N2 vaccine than patients in the low light exposure group, despite similar pre-vaccination concentrations. Sufficient seroprotective responses to all three influenza virus strains were attained for ≥ 75% of participants. These data provide first evidence for a potentially enhanced immune response in patients with dementia when they received more daily light. Increasing daily light exposure may have beneficial effects on the human immune system, either directly or via circadian rhythm stabilisation.
Bacillus subtilisYngB contributes to wall teichoic acid glucosylation and glycolipid formation during anaerobic growth
Authors: Wu Chih-Hung , Rismondo Jeanine , Morgan Rhodri M. L. , Shen Yang , Loessner Martin J. , Larrouy-Maumus Gerald , Freemont Paul S. , Gründling Angelika 
Published: December 2020

AbstractUTP-glucose-1-phosphate uridylyltransferases (UGPases) are enzymes that produce UDP-glucose from UTP and glucose-1-phosphate. InBacillus subtilis168, UDP-glucose is required for the decoration of wall teichoic acid (WTA) with glucose residues and the formation of glucolipids. TheB. subtilisUGPase GtaB is essential for UDP-glucose production under standard aerobic growth conditions, andgtaBmutants display severe growth and morphological defects. However, bioinformatics predictions indicate that two other UGPases, are present inB. subtilis. Here, we investigated the function of one of them named YngB. The crystal structure of YngB revealed that the protein has the typical fold and all necessary active site features of a functional UGPase. Furthermore, UGPase activity could be demonstratedin vitrousing UTP and glucose-1-phosphate as substrates. Expression of YngB from a synthetic promoter in aB. subtilis gtaBmutant resulted in the reintroduction of glucose residues on WTA and production of glycolipids, demonstrating that the enzyme can function as UGPasein vivo. When wild-type and mutantB. subtilisstrains were grown under anaerobic conditions, YngB-dependent glycolipid production and glucose decorations on WTA could be detected, revealing that YngB is expressed from its native promoter under anaerobic condition. Based on these findings, along with the structure of the operon containingyngBand the transcription factor thought to be required for its expression, we propose that besides WTA, potentially other cell wall components might be decorated with glucose residues during oxygen limited growth condition.
Complementary feeding practices in 80 low- and middle-income countries: prevalence and socioeconomic inequalities in dietary diversity, meal frequency and dietary adequacy
Authors: Gatica-Domínguez Giovanna , Neves Paulo A. R. , Barros Aluísio J. D. , Victora Cesar G. 
Published: December 2020

ABSTRACTObjectiveTo describe patterns and socioeconomic inequalities in complementary feeding practices among children aged 6-23 months in 80 low and middle-income countries (LMICs).MethodsWe analyzed national surveys carried out since 2010. Complementary feeding indicators for children aged 6-23 months included minimum dietary diversity (MDD), minimum meal frequency (MMF) and minimum acceptable diet (MAD). Between- and within-country inequalities were documented using relative (wealth deciles) and absolute (estimated household income) socioeconomic indicators.ResultsOnly 21.3%, 56.2% and 10.1% of the 80 countries showed prevalence levels above 50% for MDD, MMF and MAD, respectively. Western & Central Africa showed the lowest prevalence for all indicators, whereas the highest for MDD and MAD was Latin America & Caribbean, and for MMF in East Asia & the Pacific. Log per capita gross domestic product was positively associated with MDD (R2 = 48.5%), MMF (28.2%) and MAD (41.4%). Pro-rich within-country inequalities were observed in most countries for the three indicators; pro-poor inequalities were observed in two countries for MMF, and in none for the other two indicators. Breastmilk was the only type of food with a pro-poor distribution, whereas animal-source foods (dairy products, flesh foods and eggs) showed the most pronounced pro-rich inequality. Dietary diversity improved sharply when absolute annual household incomes exceeded about US$20,000. There were no consistent differences among boys and girls for any of the indicators studied.ConclusionMonitoring complementary feeding indicators in the world and implementing policies and programs to reduce wealth-related inequalities are essential to achieve optimal child nutrition.
SARS-CoV-2 infections in 171 countries and over time
Authors: Louca Stilianos 
Published: December 2020

AbstractUnderstanding the dynamics of the COVID-19 pandemic, evaluating the efficacy of past and current control measures, and estimating vaccination needs, requires knowledge of the number of infections in the population over time. This number, however, generally differs substantially from the number of confirmed cases due to a large fraction of asymptomatic infections as well as geographically and temporally variable testing effort and strategies. Here I use age-stratified death count statistics, age-dependent infection fatality risks and stochastic modeling to estimate the prevalence and growth of SARS-CoV-2 infections among adults (age ≥ 20 years) in 171 countries, from early 2020 until April 9, 2021. The accuracy of the approach is confirmed through comparison to previous nationwide general-population seroprevalence surveys in multiple countries. Estimates of infections over time, compared to reported cases, reveal that the fraction of infections that are detected vary widely over time and between countries, and hence comparisons of confirmed cases alone (between countries or time points) often yield a false picture of the pandemic’s dynamics. As of April 9, 2021, the nationwide cumulative SARS-CoV-2 prevalence (past and current infections relative to the population size) is estimated at 61% (95%-CI 42-78) for Peru, 58% (39–83) for Mexico, 57% (31–75) for Brazil, 55% (34–72) for South Africa, 29% (19-48) for the US, 26% (16–49) for the United Kingdom, 19% (12–34) for France, 19% (11–33) for Sweden, 9.6% (6.5–15) for Canada, 11% (7–19) for Germany and 0.67% (0.47–1.1) for Japan. The presented time-resolved estimates expand the possibilities to study the factors that influenced and still influence the pandemic’s progression in 171 countries. Regular updates are available at: www.loucalab.com/archive/COVID19prevalence
Shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in lipid composition inGammarus fossarum
Authors: Fu Tingting , Knittelfelder Oskar , Geffard Olivier , Clément Yohann , Testet Eric , Elie Nicolas , Touboul David , Abbaci Khedidja , Shevchenko Andrej , Lemoine Jerome , Chaumot Arnaud , Salvador Arnaud , Degli-Esposti Davide , Ayciriex Sophie 
Published: December 2020

SummarySentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the lipidome of these species is thus an essential step towards understanding the mechanism of toxicity induced by pollutants. We here extensively examined both the composition and spatial distribution of lipids in freshwater crustaceanGammarus fossarum. The baseline lipidome of gammarids of different gender and reproductive stage was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepatopancreas and their accumulation in mature oocytes. We uncovered inG. fossaruma diverse and dynamic lipid composition that deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies.
Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models
Authors: Yuin Ho Jessica Sook , Wing-Yee Mok Bobo , Campisi Laura , Jordan Tristan , Yildiz Soner , Parameswaran Sreeja , Wayman Joseph A , Gaudreault Natasha N , Meekins David A , Indran Sabarish V. , Morozov Igor , Trujillo Jessie D , Fstkchyan Yesai S , Rathnasinghe Raveen , Zhu Zeyu , Zheng Simin , Zhao Nan , White Kris , Ray-Jones Helen , Malysheva Valeriya , Thiecke Michiel J , Lau Siu-Ying , Liu Honglian , Junxia Zhang Anna , Chak-Yiu Lee Andrew , Liu Wen-Chun , Aydillo Teresa , Salom Melo Betsaida , Guccione Ernesto , Sebra Robert , Shum Elaine , Bakker Jan , Kaufman David A. , Moreira Andre L. , Carossino Mariano , Balasuriya Udeni B R , Byun Minji , Miraldi Emily R , Albrecht Randy A , Schotsaert Michael , Garcia-Sastre Adolfo , Chanda Sumit K , Jeyasekharan Anand D , TenOever Benjamin R , Spivakov Mikhail , Weirauch Matthew T , Heinz Sven , Chen Honglin , Benner Christopher , Richt Juergen A , Marazzi Ivan 
Published: December 2020

SUMMARYThe ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional,in vitroandin vivoanalyses, we report that Topoisomerase 1 (Top1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of Topotecan (TPT), a FDA-approved Top1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as four days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of Top1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing Top1 inhibitors for COVID-19 in humans.