bluuebunny/crossref_metadata_2025_split huggingface dataset:
Territory-level temperature influences breeding phenology and reproductive output in three forest passerine birds
Authors: Shutt Jack D , Bell Sophie C , Bell Fraser , Castello Joan , Harouchi Myriam El , Burgess Malcolm D 
Published: February 2021

AbstractTemperature plays an important role in determining breeding phenology of temperate birds, with higher spring temperatures associated with earlier breeding. However, the effect of localised territory-scale temperature variations is poorly understood, with relationships between temperature and breeding phenology mostly studied using coarse-grained climatic indices. Here, we interpolate spring temperatures recorded at 150 m2grid intersections encompassing 417 ha of forest to examine the influence of territory-scale temperature, and its interaction with mean annual temperature, on territory selection, breeding phenology, clutch size and fledgling success for three co-occurring single-brooded passerine birds using data from 672 nests over four years. All species exhibited significant trends in reproductive traits associated with territory-scale temperature. Pied flycatchersFicedula hypoleucasettled in cooler territories first, where they raised more fledglings. Blue titsCyanistes caeruleuslaid larger clutches in warmer territories in warm years and always laid earlier at warmer territories irrespective of annual temperature variation. Contrastingly, pied flycatcher and wood warblerPhylloscopus sibilatrixbreeding phenology was earlier at warmer territories in cool years and cooler territories in warm years, with wood warbler clutch size responding similarly to this interaction. Greater previous breeding experience and increased higher rates of historical territory occupancy (territory quality) also predicted earlier breeding phenology and higher fledging success for pied flycatchers. We suggest that the migratory pied flycatcher and wood warbler are best synchronised with their prey availability in cooler years at a local population level while resident blue tits match local phenology across all years, which is potentially advantageous under warmer predicted climate change scenarios. We conclude that temperature at the territory scale can be an important driver of settlement and breeding phenology and influence reproductive traits.
Transcriptomics-informed large-scale cortical model captures topography of pharmacological neuroimaging effects of LSD
Authors: Burt Joshua B. , Preller Katrin H. , Demirtaş Murat , Ji Jie Lisa , Krystal John H. , Vollenweider Franz X. , Anticevic Alan , Murray John D. 
Published: February 2021

AbstractPsychoactive drugs can transiently perturb brain physiology while preserving brain structure. The role of physiological state in shaping neural function can therefore be investigated through neuroimaging of pharmacologically-induced effects. This paradigm has revealed that neural and experiential effects of lysergic acid diethylamide (LSD) are attributable to its agonist activity at the serotonin-2A receptor. Here, we integrate brainwide transcriptomics with biophysically-based large-scale circuit modeling to simulate acute neuromodulatory effects of LSD on human cortical dynamics. Our model captures the topographic effects of LSD-induced changes in cortical BOLD functional connectivity. These findings suggest that serotonin-2A-mediated modulation of pyramidal cell gain is the circuit mechanism through which LSD alters cortical functional topography. Individual-subject fitting reveals that the model captures patterns of individual neural differences in drug response that predict altered states of consciousness. This work establishes a framework for linking molecular-level manipulations to salient changes in brain function, with implications for precision medicine.
Mn2+coordinates Cap-0-RNA to align substrates for efficient 2′-O-methyl transfer by SARS-CoV-2 nsp16
Authors: Minasov George , Rosas-Lemus Monica , Shuvalova Ludmilla , Inniss Nicole L. , Brunzelle Joseph S. , Daczkowski Courtney M. , Hoover Paul , Mesecar Andrew D. , Satchell Karla J. F. 
Published: February 2021

AbstractCapping viral messenger RNAs is essential for efficient translation and prevents their detection by host innate immune responses. For SARS-CoV-2, RNA capping includes 2′-O-methylation of the first ribonucleotide by methyltransferase nsp16 in complex with activator nsp10. The reaction requires substrates, a short RNA and SAM, and is catalyzed by divalent cations, with preference for Mn2+. Crystal structures of nsp16-nsp10 with capped RNAs revealed a critical role of metal ions in stabilizing interactions between ribonucleotides and nsp16, resulting in precise alignment of the substrates for methyl transfer. An aspartate residue that is highly conserved among coronaviruses alters the backbone conformation of the capped RNA in the binding groove. This aspartate is absent in mammalian methyltransferases and is a promising site for designing coronavirus-specific inhibitors.
Multiplexed activation in mammalian cells using dFnCas12a-VPR
Authors: Bryson James W. , Auxillos Jamie Y. , Rosser Susan J. 
Published: February 2021

AbstractThe adoption of CRISPR systems for the generation of synthetic transcription factors has greatly simplified the process for upregulating endogenous gene expression, with a plethora of applications in cell biology, bioproduction and cell reprogramming. In particular the recently discovered Cas12a systems offer extended potential, as Cas12a is capable of processing its own crRNA array to provide multiple individual crRNAs for subsequent targeting from a single transcript. Here we show the application of dFnCas12a-VPR in mammalian cells, with FnCas12a possessing a shorter PAM sequence than As or Lb variants, enabling denser targeting of genomic loci. We observe that synergistic activation and multiplexing can be achieved using crRNA arrays but also show that crRNAs expressed towards the 5’ of 6-crRNA arrays show evidence of enhanced activity. This not only represents a more flexible tool for transcriptional modulation but further expands our understanding of the design capabilities and limitations when considering longer crRNA arrays for multiplexed targeting.
CSF metabolites associate with CSF tau and improve prediction of Alzheimer’s disease status
Authors: Dong Ruocheng , Darst Burcu F. , Deming Yuetiva , Ma Yue , Lu Qiongshi , Zetterberg Henrik , Blennow Kaj , Carlsson Cynthia M. , Johnson Sterling C. , Asthana Sanjay , Engelman Corinne D. 
Published: February 2021

AbstractINTRODUCTIONCerebrospinal fluid (CSF) total tau (t-tau) and phosphorylated tau (p-tau) are biomarkers of Alzheimer’s disease (AD), yet much is unknown about AD-associated changes in tau metabolism and tau tangle etiology.METHODSWe assessed the variation of t-tau and p-tau explained by 38 previously identified CSF metabolites using linear regression models in middle-age controls from the Wisconsin Alzheimer’s Disease Research Center, and predicted AD/mild cognitive impairment (MCI) vs. an independent set of older controls using metabolites selected by the least absolute shrinkage and selection operator (LASSO).RESULTSThe 38 CSF metabolites explained 70.3% and 75.7% of the variance in t-tau and p-tau. Of these, 7 LASSO-selected metabolites improved the prediction ability of AD/MCI vs. older controls (AUC score increased from 0.92 to 0.97 and 0.78 to 0.93) compared to the base model.DISCUSSIONThese tau-correlated CSF metabolites increase AD/MCI prediction accuracy and may provide insight into tau tangle etiology.
Risk factors for SARS-CoV-2 infection among farmworkers in Monterey County, California
Authors: Mora Ana M. , Lewnard Joseph A. , Kogut Katherine , Rauch Stephen A. , Morga Norma , Hernandez Samantha , Wong Marcus P. , Huen Karen , Chang Cynthia , Jewell Nicholas P. , Holland Nina , Harris Eva , Cuevas Maximiliano , Eskenazi Brenda 
Published: February 2021

ABSTRACTImportanceEssential workers in agriculture and food production have been severely affected by the ongoing COVID-19 pandemic.ObjectiveTo identify risk factors associated with SARS-CoV-2 shedding and antibody response in farmworkers in California.DesignThis cross-sectional study collected survey data and determined current SARS-CoV-2 shedding and seropositivity among 1,107 farmworkers in California’s Salinas Valley from 16 July to 30 November 2020.SettingFarmworkers receiving transcription-mediated amplification (TMA) tests for SARS-CoV-2 infection at federally qualified community clinics and community sites were invited to participate in our study.ParticipantsIndividuals were eligible if they were not pregnant, ≥18 years old, had conducted farm work since the pandemic started, and were proficient in English or Spanish.ExposuresSociodemographic, household, community, and workplace characteristics.Main Outcome(s) and Measure(s)Current (as indicated by TMA positivity) and historical (as indicated by IgG seropositivity) SARS-CoV-2 infection.ResultsMost farmworkers enrolled in the study were born in Mexico, had primary school or lower levels of educational attainment, and were overweight or obese. Current SARS-CoV-2 shedding was associated in multivariable analyses with attained only primary or lower educational levels (RR=1.32; 95% CI: 0.99-1.76), speaking an indigenous language at home (RR=1.30; 0.97-1.73), working in the fields (RR=1.60; 1.03-2.50), and exposure to known or suspected COVID-19 case at home (RR=2.98; 2.06-4.32) or in the workplace (RR=1.59; 1.18-2.14). Antibody detection was associated with residential exposures including living in crowded housing (RR=1.23; 0.98-1.53), with children (RR=1.40; 1.1-1.76) or unrelated roommates (RR=1.40; 1.19-1.64), and with a known or suspected COVID-19 case (RR=1.59; 1.13-2.24). Those who were obese (RR=1.65; 1.01-2.70) or diabetic (RR=1.31; 0.98-1.75) were also more likely to be seropositive. Farmworkers who lived in rural areas other than Greenfield (RR=0.58; 0.47-0.71), worked indoors (RR=0.68; 0.61-0.77), or whose employer provided them with information on how to protect themselves at work (RR=0.59; 0.40-0.86) had lower risk of prior infection.Conclusions and RelevanceOur findings suggest both residential and workplace exposures are contributing to SARS-CoV-2 infection among farmworkers in California. Urgent distribution of COVID-19 vaccines is warranted given this population’s increased risk of infection and the essential nature of their work.
Hierarchical modelling of functional brain networks in population and individuals from big fMRI data
Authors: Farahibozorg Seyedeh-Rezvan , Bijsterbosch Janine D , Gong Weikang , Jbabdi Saad , Smith Stephen M , Harrison Samuel J , Woolrich Mark W 
Published: February 2021

AbstractA major goal of large-scale brain imaging datasets is to provide resources for investigating heterogeneous populations. Characterisation of functional brain networks for individual subjects from these datasets will have an enormous potential for prediction of cognitive or clinical traits. We propose for the first time a technique, Stochastic Probabilistic Functional Modes (sPROFUMO), that is scalable to UK Biobank (UKB) with expected 100,000 participants, and hierarchically estimates functional brain networks in individuals and the population, while allowing for bidirectional flow of information between the two. Using simulations, we show the model’s utility, especially in scenarios that involve significant cross-subject variability, or require delineation of fine-grained differences between the networks. Subsequently, by applying the model to resting-state fMRI from 4999 UKB subjects, we mapped resting state networks (RSNs) in single subjects with greater detail than has been possible previously in UKB (>100 RSNs), and demonstrate that these RSNs can predict a range of sensorimotor and higher-level cognitive functions. Furthermore, we demonstrate several advantages of the model over independent component analysis combined with dual-regression (ICA-DR), particularly with respect to the estimation of the spatial configuration of the RSNs and the predictive power for cognitive traits. The proposed model and results can open a new door for future investigations into individualised profiles of brain function from big data.HighlightsWe introduce stochastic PROFUMO (sPROFUMO) for inferring functional brain networks from big datasPROFUMO hierarchically estimates fMRI networks for the population and every individualWe characterised high dimensional resting state fMRI networks from UK BiobankModel outperforms ICA and dual regression for estimation of individual-specific network topographyWe demonstrate the model’s utility for predicting cognitive traits, and capturing subject variability in network topographies versus connectivity
PACAS: pairwise comparisons of aligned subsequences
Authors: DeMonn Kenneth , Powell Christopher L. E. , Battistuzzi Fabia U. 
Published: February 2021

AbstractEvaluation of conservation levels of alignments is a pivotal step for evolutionary analyses. Commonly used software to analyze alignments produce either site-by-site or overall measures of conservation without the ability of performing comparative analyses among sub-regions of the alignment. We have developed a stand-alone alignment analyzer (PairwiseComparisons ofAlignedSubsequences) that uses user-defined sub-regions to report various measures of conservation among pairs of sequences and between the sub-regions and the rest of the alignment. We then used this method to analyze the repetitive regions (low complexity regions; LCRs) of two genes in Plasmodium: AMA1 and CSP. We found that LCRs are not always associated with high entropy (low conservation) suggesting that some LCRs may be less likely to mutate than others.Availability and ImplementationPACAS is publicly available athttps://github.com/BlabOaklandU/PACASContactFabia U. Battistuzzibattistu@oakland.eduSupplementary informationn/a
Rapid fall in circulating non-classical monocytes in ST elevation myocardial infarction patients correlates with cardiac injury
Authors: Marsh Sarah A. , Park Catherine , Redgrave Rachael E. , Singh Esha , Draganova Lilia , Boag Stephen E. , Spray Luke , Ali Simi , Spyridopoulos Ioakim , Arthur Helen M. 
Published: February 2021

AbstractObjectiveMyocardial infarction leads to a rapid innate immune response that is ultimately required for repair of damaged heart tissue. We therefore examined circulating monocyte dynamics immediately after reperfusion of the culprit coronary vessel in STEMI patients to determine whether this correlated with level of cardiac injury. A mouse model of cardiac ischaemia/reperfusion injury was subsequently used to establish the degree of monocyte margination to the coronary vasculature that could potentially contribute to the drop in circulating monocytes.Approach and ResultsWe retrospectively analysed blood samples from 51 STEMI patients to assess the number of non-classical (NC), classical and intermediate monocytes immediately following primary percutaneous coronary intervention. Classical and intermediate monocytes showed minimal change. On the other hand circulating numbers of NC monocytes fell by approximately 50% at 90 minutes post-reperfusion. This rapid decrease in NC monocytes was greatest in patients with the largest infarct size (p<0.05) and correlated inversely with left ventricular function (r=0.41, p=0.04). The early fall in NC monocytes post reperfusion was confirmed in a second prospective study of 13 STEMI patients. Furthermore, in a mouse cardiac ischaemia model, there was significant monocyte adhesion to coronary vessel endothelium at 2 hours post-reperfusion pointing to a specific and rapid vessel margination response to cardiac injury.ConclusionsRapid depletion of NC monocytes from the circulation in STEMI patients following coronary artery reperfusion correlates with the level of acute cardiac injury and involves rapid margination to the coronary vasculature.Graphical AbstractHighlights3-5 bullet points that summarize the major findings of the study.Circulating non classical monocytes show a rapid fall in STEMI patients within 90 minutes of re-opening the culprit coronary artery.The extent of the drop in non classical monocytes correlates with loss of cardiac function and increased infarct size.A mouse model of cardiac ischaemia and reperfusion shows rapid margination of monocytes to the coronary vasculature
The conserved serine transporter SdaC moonlights to enable self recognition
Authors: Chittor Achala , Gibbs Karine A. 
Published: February 2021

AbstractCells can use self recognition to achieve cooperative behaviors. Self-recognition genes principally evolve in tandem with partner self-recognition alleles. However, other constraints on protein evolution could exist. Here, we have identified an interaction outside of self-recognition loci that could constrain the sequence variation of a self-recognition protein. We show that during collective swarm expansion inProteus mirabilis, self-recognition signaling co-opts SdaC, a serine transporter. Serine uptake is crucial for bacterial survival and colonization. Single-residue variants of SdaC reveal that self recognition requires an open conformation of the protein; serine transport is dispensable. A distant ortholog fromEscherichia coliis sufficient for self recognition; however, a homologous serine transporter, YhaO, is not. Thus, SdaC couples self recognition and serine transport, likely through a shared molecular interface. Understanding molecular and ecological constraints on self-recognition proteins can provide insights into the evolution of self recognition and emergent collective behaviors.Abstract Figure
Energy content of anchovy and sardine using surrogate calorimetry methods
Authors: Campanini Claudia , Albo-Puigserver Marta , Gérez Sara , Lloret-Lloret Elena , Giménez Joan , Pennino Maria Grazia , Bellido Jose Maria , Colmenero Ana I. , Coll Marta 
Published: February 2021

AbstractEuropean anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) are crucial species for the marine ecosystem of the Northwestern Mediterranean Sea. They account for a high percentage of fish landings and they represent an important economic income. Concerns over their stock status are rising in recent years as biomass, growth, reproductive capacity and body condition of both species are declining. Therefore, there is an urgent need for a continuous and fast body condition monitoring scheme. Energy storage variability has important implications for both fish recruitment and population structure. Direct condition indices, such as bomb calorimetry, are highly reliable for measuring the energy content, but extremely time-consuming. Alternatively, fatmeter analysis and relative condition index (Kn) have been proposed as effective indirect methods. The aim of this study is to test the application of fatmeter as a surrogate of bomb calorimetry to infer the energy content of both small pelagic fishes. For the validation, fatmeter values were compared with both energy density (ED; via bomb calorimetry) and Kn values. Individuals of both species were sampled monthly in Barcelona harbor for a year in order to assess seasonal variations in energy content. Our results highlight that fatmeter measurements are strongly correlated with calorimetry for sardine, while a weaker but significant correlation was found for anchovy. The observed differences between the two species are related to their breeding strategies. Based on this study, fatmeter analysis appears to be a faster and suitable method to evaluate the energy content of both species routinely., In addition, we provide a linear model to infer ED from fatmeter values of both small pelagic fish. Eventually, these findings could allow for the avoidance of bomb calorimetry and could be used to implement body condition monitoring protocols, and to boost continuous large-scale monitoring.
Input-independent homeostasis of developing thalamocortical activity
Authors: Riyahi Pouria , Phillips Marnie A , Colonnese Matthew T 
Published: February 2021

ABSTRACTThe isocortex of all mammals studied to date shows a progressive increase in the amount and continuity of background activity during early development. In humans the transition from a discontinuous (mostly silent, intermittently bursting) cortex to one that is continuously active is complete soon after birth and is a critical prognostic indicator in newborns. In the visual cortex of rodents this switch from discontinuous to continuous background activity occurs rapidly during the two days before eye-opening, driven by activity changes in relay thalamus. The factors that regulate the timing of continuity development, which enables mature visual processing, are unknown. Here we test the role of the retina, the primary input, in the development of continuous spontaneous activity in the visual system of mice using depth electrode recordings of cortical activity from enucleated micein vivo. Bilateral enucleation at postnatal day (P)6, one week prior to the onset of continuous activity, acutely silences cortex, yet firing rates and early oscillations return to normal within two days and show a normal developmental trajectory through P12. Enucleated animals showed differences in silent period duration and continuity on P13 that resolved on P16, and an increase in low frequency power that did not. Our results show that the timing of cortical activity development isnotdetermined by the major driving input to the system. Rather, homeostatic mechanisms in thalamocortex regulate firing rates and continuity even across periods of rapid maturation.
Genome-wide analysis of the apple family 1 glycosyltransferases identified a flavonoid-modifying UGT, MdUGT83L3, which is targeted by MdMYB88 and contributes to stress adaptation
Authors: Li Yanjie , Li Pan , Zhang Lei , Shu Jing , Court Michael H , Sun Zhuojing , Jiang Lepu , Zheng Chengchao , Shu Huairui , Hou Bingkai , Ji Lusha , Zhang Shizhong 
Published: February 2021

AbstractNowadays, the plant family 1 UDP-glycosyltransferases (UGTs) are more and more investigated owing to their contribution to the plant secondary metabolism and diverse biological roles. Apple (Malus domestica) is one of the most widely cultivated fruit trees with great economical importance. However, poor knowledge is known about the apple UGTs. In this study, we identified 229 members of family 1 through a genome-wide analysis of the apple UGTs, which were clustered into 18 groups, from A to R. We also performed detailed analysis to 34 apple UGTs with quantitavive RT-PCR, and discovered a number of stress-regulated UGTs. Among them, we characterized the role of MD09G1064900, also named as MdUGT83L3, which is significantly induced by salt and cold. In vivo analysis showed that it has high activity towards cyanidin, and moderate activity towards quercetin and keampferol. The transgenic callus and regenerated apple plants overexpressing MdUGT83L3 showed enhanced tolerance to salt and cold treatments. Overexpression of MdUGT83L3 also increased anthocyanin accumulation in the callus tissues and enhanced ROS clearing upon exposed to salt and cold stresses. Futhermore, via yeast-two-hybrid assay, EMSA and CHIP analysis, we also found that MdUGT83L3 could be directly regualted by MdMYB88. Our study indicated that MdUGT83L3, under the regulation of MdMYB88, plays important roles in salt and cold stress adaptation via modulating flavonoid metabolism in apple.