bluuebunny/crossref_metadata_2025_split huggingface dataset:
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa
Authors: Zhu Jie , Tian Liu , Chen Peishan , Han Mo , Song Liju , Tong Xin , Sun Xiaohuan , Yang Fangming , Lin Zhipeng , Liu Xing , Liu Chuan , Wang Xiaohan , Lin Yuxiang , Cai Kaiye , Hou Yong , Xu Xun , Yang Huanming , Wang Jian , Kristiansen Karsten , Xiao Liang , Zhang Tao , Jia Huijue , Jie Zhuye 
Published: September 2021

Abstract
The oral cavity of each person is home to hundreds of bacterial species. While taxa for oral diseases have been studied using culture-based characterization as well as amplicon sequencing, metagenomic and genomic information remains scarce compared to the fecal microbiome. Here, using metagenomic shotgun data for 3346 oral metagenomic samples together with 808 published samples, we obtain 56,213 metagenome-assembled genomes (MAGs), and more than 64% of the 3589 species-level genome bins (SGBs) contain no publicly available genomes. The resulting genome collection is representative of samples around the world and contains many genomes from candidate phyla radiation (CPR) that lack monoculture. Also, it enables the discovery of new taxa such as a genus Candidatus Bgiplasma within the family Acholeplasmataceae. Large-scale metagenomic data from massive samples also allow the assembly of strains from important oral taxa such as Porphyromonas and Neisseria. The oral microbes encode genes that could potentially metabolize drugs. Apart from these findings, a strongly male-enriched Campylobacter species was identified. Oral samples would be more user-friendly collected than fecal samples and have the potential for disease diagnosis. Thus, these data lay down a genomic framework for future inquiries of the human oral microbiome.
GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction
Authors: Wang Jiabo , Zhang Zhiwu 
Published: September 2021

Abstract
Genome-wide association study (GWAS) and genomic prediction/selection (GP/GS) are the two essential enterprises in genomic research. Due to the great magnitude and complexity of genomic and phenotypic data, analytical methods and their associated software packages are frequently advanced. GAPIT is a widely-used genomic association and prediction integrated tool as an R package. The first version was released to the public in 2012 with the implementation of the general linear model (GLM), mixed linear model (MLM), compressed MLM (CMLM), and genomic best linear unbiased prediction (gBLUP). The second version was released in 2016 with several new implementations, including enriched CMLM (ECMLM) and settlement of MLMs under progressively exclusive relationship (SUPER). All the GWAS methods are based on the single-locus test. For the first time, in the current release of GAPIT, version 3 implemented three multi-locus test methods, including multiple loci mixed model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK). Additionally, two GP/GS methods were implemented based on CMLM (named compressed BLUP; cBLUP) and SUPER (named SUPER BLUP; sBLUP). These new implementations not only boost statistical power for GWAS and prediction accuracy for GP/GS, but also improve computing speed and increase the capacity to analyze big genomic data. Here, we document the current upgrade of GAPIT by describing the selection of the recently developed methods, their implementations, and potential impact. All documents, including source code, user manual, demo data, and tutorials, are freely available at the GAPIT website (http://zzlab.net/GAPIT).
Hydrothermal Cooling as a Requirement for Short Storage of Silicic Magmas
Authors: Kelly Liam J. , Gualda Guilherme A. R. , Gravley Darren M. , Dempsey David E. 
Published: September 2021

AbstractLarge (>50 km3) magma bodies that contribute to caldera‐forming eruptions in the Taupō Volcanic Zone (TVZ), New Zealand have shown evidence for crystallization and storage on the order of decades to centuries prior to eruption. We compare various conductive and convective heat extraction models to determine which is more likely to enable the heat loss required for short magma storage. We conclude that purely conductive models only account for heat loss on millennial or longer timescales. We also show that convective hydrothermal systems with heat output of 1,000 MW in magnitude are required for decadal heat extraction from a large, contiguous magma body; yet, heat output similar to present‐day conditions would be suitable for cooling magma distributed as a patchwork of smaller magma bodies. This study shows the potential connection with heat flow at the surface and the presence of a magma body, providing future directions for monitoring restless calderas in environments with a wealth of hydrothermal activity like the TVZ.
Characteristics of Foreshocks Revealed by an Earthquake Forecasting Method Based on Precursory Swarm Activity
Authors: Hirose F. , Tamaribuchi K. , Maeda K. 
Published: September 2021

AbstractWe have developed an empirical earthquake forecast method, Maeda's method, based on the statistical features of precursory seismic swarm activity, that is foreshocks, which sometimes appear before a mainshock, and issuing an alert of a mainshock occurrence within a certain period of time. In this study, we investigated the effectiveness of earthquake forecast of Maeda's method by applying it to seismicity under various tectonic environments of Japan such as regions characterized by interplate seismic activity, a tectonic fault line (concentrated deformation zone), and an island arc area of seismic and volcanic activity. As a result, we confirmed that Maeda's method yielded generally higher scores than a forecast model based on a stationary space‐time epidemic‐type aftershock sequence (ETAS) model. We also found that foreshocks detected along the Japan Trench were distributed along the edges of low‐velocity anomalies and among areas with background swarms related to slow slip events (SSEs). The foreshocks may have been caused by a heterogeneous stress distribution associated with the existence of a plate‐bending axis and a subducted seamount. Foreshocks off Iwate prefecture, in particular, were excited by periodic SSEs. In an inland tectonic zone and an island arc, swarm activity associated with magmatic or fluid activity related to low‐velocity anomalies tended to be followed by a mainshock. Maeda's method is a simple and efficient counting‐number‐based earthquake forecast model and may capture characteristics of foreshocks that reflect a physical phenomenon, such as a nucleation process involving precursory slip, which the stationary ETAS model is not able to represent.
Hypocenter Hotspots Illuminated Using a New Cross‐Correlation‐Based Hypocenter and Centroid Relocation Method
Authors: Chang Ta‐Wei , Ide Satoshi 
Published: September 2021

AbstractAccurate earthquake locations are important for understanding earthquake processes. Recent advances in earthquake relocation methods have resulted in relative centroid locations with smaller uncertainties using cross‐correlation‐based methods. However, relative hypocenter locations, which are traditionally determined using the onset times of event waveforms, generally possess larger uncertainties than that of the centroids. Here, we develop a new cross‐correlation‐based relative hypocenter relocation method based on the network correlation coefficient method, whereby we incorporate an additional step to search for a suitable window to cross‐correlate the event waveform onsets. We then perform a joint inversion on the obtained relative hypocenter and centroid locations to directly compare their relative locations under a unified coordinate. We apply this method to three regions where repeating earthquakes have been detected, and reveal both the repetitive rupture of similar centroids by these repeating events and newly illuminated hypocenter hotspots that serve as the onset region of earthquakes that grow into different but selective magnitudes. Our joint analysis of hypocenter and centroid locations enables quick estimations of rupture propagation directions without the need to perform slip inversion analyses. We estimate the location uncertainties via bootstrapping, with the 95% confidence intervals yielding sub‐100 m horizontal uncertainties in both the centroid and hypocenter locations with the best station coverage and event availability. These results point to limited but existing correspondence between the hypocenter and centroid locations and the earthquake magnitudes, as well as complexity in the hypocenter distributions, even within repeating earthquake sequences whose rupture areas largely overlap.
Complex Migration of Tremor Near Cholame, CA, Resolved by Seismic Array Analysis
Authors: Inbal A. , Thomas A. M. , Newton T. , Bürgmann R. 
Published: September 2021

AbstractTectonic tremor observed along the Cholame and Parkfield sections of the San Andreas Fault has previously been associated with transient slip beneath the seismogenic zone. To study tremor and associated Low Frequency Earthquakes (LFEs), we deployed three dense near‐fault seismic arrays for a period of 3 months in 2018. In early August 2018, the arrays recorded a strong 4‐day‐long deep transient that nucleated in Cholame and propagated toward the northwest. The initiation area is characterized by tremor that persists throughout the transient, while adjacent fault portions located to the northwest host more intermittent tremor. From the rate and location of tremor and LFEs, we infer a deep slip transient, whose along‐strike propagation velocity is ∼8 km/day. Secondary tremor fronts are observed to travel ahead of the main slow slip front at speeds that are times faster. These rapid migrations propagate in slow slip events (SSE) slip‐parallel direction, and are sometimes observed to back‐propagate into previously ruptured segments. High‐resolution images of secondary fronts obtained by using near‐fault borehole stations indicate the active tremor band takes the shape of a narrow strain pulse that is bounded from above by the lower edge of the seismogenic zone. We estimate the stress drops associated with the secondary slip fronts are of the order of a few kPa. Frequency‐dependent analysis suggests the tremor signal is coherent at frequencies as high as 16 Hz, and that the spatial distribution of high‐ and low‐frequency tremor radiators is sometimes complementary.
Chemical Tomography in a Fresh Wildland Fire Plume: A Large Eddy Simulation (LES) Study
Authors: Wang Siyuan , Coggon Matthew M. , Gkatzelis Georgios I. , Warneke Carsten , Bourgeois Ilann , Ryerson Thomas , Peischl Jeff , Veres Patrick R. , Neuman J. Andrew , Hair Johnathan , Shingler Taylor , Fenn Marta , Diskin Glenn , Huey L. Greg , Lee Young Ro , Apel Eric C. , Hornbrook Rebecca S. , Hills Alan J. , Hall Samuel R. , Ullmann Kirk , Bela Megan M. , Trainer Michael K. , Kumar Rajesh , Orlando John J. , Flocke Frank M. , Emmons Louisa K. 
Published: September 2021

AbstractWildland fires involve complicated processes that are challenging to represent in chemical transport models. Recent airborne measurements reveal remarkable chemical tomography in fresh wildland fire plumes, which remain yet to be fully explored using models. Here, we present a high‐resolution large eddy simulation model coupled to chemistry to study the chemical evolution in fresh wildland fire plume. The model is configured for a large fire heavily sampled during the Fire Influence on Regional to Global Environments and Air Quality field campaign, and a variety of airborne measurements are used to evaluate the chemical heterogeneity revealed by the model. We show that the model captures the observed cross‐transect variations of a number of compounds quite well, including ozone (O3), nitrous acid (HONO), and peroxyacetyl nitrate. The combined observational and modeling results suggest that the top and edges of fresh plume drive the photochemistry, while dark chemistry is also present but in the lower part of the plume. The model spatial resolution is shown to be very important as it may shift the chemical regime, leading to biases in O3 and NOx chemistry. Based on findings in this work, we speculate that the impact of small fires on air quality may be largely underestimated in models with coarse spatial resolutions.
Interoception and obesity: a systematic review and meta-analysis of the relationship between interoception and BMI
Authors: Robinson Eric , Foote Georgia , Smith Jemma , Higgs Suzanne , Jones Andrew 
Published: September 2021

Abstract
Background
Interoception refers to the processes by which we sense, interpret and integrate signals originating from within the body. Deficits in interoception have been linked to higher BMI and may contribute to weight gain. However, there have been conflicting findings and it is not clear how higher BMI is associated with different facets of interoception, such as interoceptive accuracy (the ability to detect internal signals) and sensibility (the tendency to attend to internal signals).

Methods
We conducted a systematic review and meta-analysis of studies that measured interoception and BMI. We examined relationships between interoception and BMI in children and adults separately and as a function of interoceptive facet and measure. In sensitivity analyses, we tested for evidence of publication bias and whether the results were consistent when studies with a high risk of bias were excluded.

Results
A total of 87 articles were eligible for inclusion. In adults (121 effects, 10,425 participants), there was cross-sectional evidence of higher BMI being associated with overall deficits in interoception (r = −0.054, 95% CI: −0.084 to −0.025) and this was consistent across sensitivity analyses. There was no statistically significant evidence of moderation by interoceptive facet or measure, although there was some variability in effect size estimates based on interoceptive facet and measures. A smaller meta-analysis limited to studies that compared participants with normal weight vs. overweight/obesity indicated poorer interoception in participants with overweight/obesity (SMD = −0.39, 95% CI −0.60 to −0.18).

Conclusions
In cross-sectional studies, deficits in interoception are associated with higher BMI. However, it remains unclear whether deficits in interoception contribute to or are a consequence of weight gain and obesity.
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom
Authors: McCain J Scott P , Allen Andrew E , Bertrand Erin M 
Published: September 2021

Abstract
Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.
Emerging imaging methods to study whole-brain function in rodent models
Authors: Markicevic Marija , Savvateev Iurii , Grimm Christina , Zerbi Valerio 
Published: September 2021

AbstractIn the past decade, the idea that single populations of neurons support cognition and behavior has gradually given way to the realization that connectivity matters and that complex behavior results from interactions between remote yet anatomically connected areas that form specialized networks. In parallel, innovation in brain imaging techniques has led to the availability of a broad set of imaging tools to characterize the functional organization of complex networks. However, each of these tools poses significant technical challenges and faces limitations, which require careful consideration of their underlying anatomical, physiological, and physical specificity. In this review, we focus on emerging methods for measuring spontaneous or evoked activity in the brain. We discuss methods that can measure large-scale brain activity (directly or indirectly) with a relatively high temporal resolution, from milliseconds to seconds. We further focus on methods designed for studying the mammalian brain in preclinical models, specifically in mice and rats. This field has seen a great deal of innovation in recent years, facilitated by concomitant innovation in gene-editing techniques and the possibility of more invasive recordings. This review aims to give an overview of currently available preclinical imaging methods and an outlook on future developments. This information is suitable for educational purposes and for assisting scientists in choosing the appropriate method for their own research question.
The link between attention deficit hyperactivity disorder (ADHD) symptoms and obesity-related traits: genetic and prenatal explanations
Authors: Karhunen Ville , Bond Tom A. , Zuber Verena , Hurtig Tuula , Moilanen Irma , Järvelin Marjo-Riitta , Evangelou Marina , Rodriguez Alina 
Published: September 2021

AbstractAttention-deficit/hyperactivity disorder (ADHD) often co-occurs with obesity, however, the potential causality between the traits remains unclear. We examined both genetic and prenatal evidence for causality using Mendelian Randomisation (MR) and polygenic risk scores (PRS). We conducted bi-directional MR on ADHD liability and six obesity-related traits using summary statistics from the largest available meta-analyses of genome-wide association studies. We also examined the shared genetic aetiology between ADHD symptoms (inattention and hyperactivity) and body mass index (BMI) by PRS association analysis using longitudinal data from Northern Finland Birth Cohort 1986 (NFBC1986, n = 2984). Lastly, we examined the impact of the prenatal environment by association analysis of maternal pre-pregnancy BMI and offspring ADHD symptoms, adjusted for PRS of both traits, in NFBC1986 dataset. Through MR analyses, we found evidence for bidirectional causality between ADHD liability and obesity-related traits. PRS association analyses showed evidence for genetic overlap between ADHD symptoms and BMI. We found no evidence for a difference between inattention and hyperactivity symptoms, suggesting that neither symptom subtype is driving the association. We found evidence for association between maternal pre-pregnancy BMI and offspring ADHD symptoms after adjusting for both BMI and ADHD PRS (association p-value = 0.027 for inattention, p = 0.008 for hyperactivity). These results are consistent with the hypothesis that the co-occurrence between ADHD and obesity has both genetic and prenatal environmental origins.
The association between BDNF levels and risperidone-induced weight gain is dependent on the BDNF Val66Met polymorphism in antipsychotic-naive first episode schizophrenia patients: a 12-week prospective study
Authors: Liu Jiahong , Wang Pingping , Sun Leilei , Guan Xiaoni , Xiu Meihong , Zhang Xiangyang 
Published: September 2021

AbstractA growing number of studies have shown that brain-derived neurotrophic factor (BDNF) is associated with weight gain during antipsychotic treatment in schizophrenia patients. However, there is still a lack of research results in the initial stage of antipsychotic treatment. This study aimed to evaluate the relationship between weight gain caused by risperidone monotherapy for 12 weeks and BDNF level in antipsychotic-naive and first-episode (ANFE) patients with schizophrenia, and we hypothesize that this may depend on BDNF Val66Met gene polymorphism. In a 12-week longitudinal trial, 225 ANFE patients were enrolled and treated with risperidone. Body weight was measured at baseline and during the 12-week follow-up. After treatment, the average weight of ANFE patients increased by 2.6 kg. Furthermore, we found that in patients with Val/Val genotype, the increase in serum BDNF levels was negatively correlated with risperidone-induced weight gain (r = −0.44, p = 0.008). Regression analysis showed that the baseline BDNF level was a predictor of weight gain after treatment (β = −0.45, t = −3.0, p = 0.005). Our results suggest that the BDNF signaling may be involved in weight gain caused by risperidone treatment. Furthermore, the negative association between weight gain and increased BDNF levels during risperidone treatment in ANFE schizophrenia depends on the BDNF Val66Met polymorphism.
The metabolic flexibility of quiescent CSC: implications for chemotherapy resistance
Authors: Chen Kangchen , Zhang Chenzhi , Ling Sunbin , Wei Rongli , Wang Jianguo , Xu Xiao 
Published: September 2021

AbstractQuiescence has been observed in stem cells (SCs), including adult SCs and cancer SCs (CSCs). Conventional chemotherapies mostly target proliferating cancer cells, while the quiescent state favors CSCs escape to chemotherapeutic drugs, leaving risks for tumor recurrence or metastasis. The tumor microenvironment (TME) provides various signals that maintain resident quiescent CSCs, protect them from immune surveillance, and facilitates their recurrence potential. Since the TME has the potential to support and initiate stem cell-like programs in cancer cells, targeting the TME components may prove to be a powerful modality for the treatment of chemotherapy resistance. In addition, an increasing number of studies have discovered that CSCs exhibit the potential of metabolic flexibility when metabolic substrates are limited, and display increased robustness in response to stress. Accompanied by chemotherapy that targets proliferative cancer cells, treatments that modulate CSC quiescence through the regulation of metabolic pathways also show promise. In this review, we focus on the roles of metabolic flexibility and the TME on CSCs quiescence and further discuss potential treatments of targeting CSCs and the TME to limit chemotherapy resistance.