bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in the high-latitude mesosphere temperature and mesopause revealed by SABER
Authors: Liu Xiao , Xu Jiyao , Yue Jia , Liu Yangkun , Andrioli Vania F. 
Published: September 2024

Abstract. The temperature trend in the mesosphere and lower-thermosphere (MLT) region can be regarded as an indicator of climate change. Using temperature profiles measured by the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument during 2002–2023 and binning them based on the yaw cycle, we obtain a continuous dataset with a wide local time coverage at 50° S–80° N or 80° S–50° N. The seasonal change in temperature, caused by the forward drift in the SABER yaw cycle, is removed using the climatological temperature of the Naval Research Laboratory's Mass Spectrometer Incoherent Scatter Radar model (MSIS2.0). The corrected temperature without any waves is regarded as the mean temperature. At 50° S–50° N, the cooling trends in the mean temperature are significant in the MLT region and are in agreement with previous studies. The novel finding is that the cooling trends of ≥ l2 K per decade exhibit seasonal symmetry and reach peaks of ≥ 6 K per decade at high latitudes around the summer solstice. Moreover, there are warming trends of 1–2.5 K per decade at an altitude range of 10−2–10−3 hPa, specifically at latitudes higher than 55° N in October and December and at latitudes higher than 55° S in April and August. Over the past 22 years, the mesopause temperature (altitude) in the northern summer polar region has been ∼ 5–11 K (∼ 1 km) colder (lower) than that in the corresponding southern region. The trends in the mesopause temperature are dependent on latitudes and months, but they are negative at most latitudes and reach larger magnitudes at high latitudes. These results indicate that the temperature in the high-latitude MLT region is more sensitive to dynamic changes.
The SDUST2022GRA global marine gravity anomalies recovered from radar and laser altimeter data: contribution of ICESat-2 laser altimetry
Authors: Li Zhen , Guo Jinyun , Zhu Chengcheng , Liu Xin , Hwang Cheinway , Lebedev Sergey , Chang Xiaotao , Soloviev Anatoly , Sun Heping 
Published: September 2024

Abstract. The global marine gravity anomaly model is predominantly recovered from along-track radar altimeter data. Despite significant advances in gravity anomaly recovery, the improvement of the gravity anomaly model remains constrained by the absence of cross-track geoid gradients and the reduction in radar altimeter data, especially in coastal and high-latitude regions. ICESat-2 laser altimetry, with a three-pair laser beam configuration, a small footprint, and a near-polar orbit, facilitates the determination of cross-track geoid gradients and provides valid observations in certain regions. We present an ICESat-2 altimeter data processing strategy that includes the determination of cross-track geoid gradients and the combination of along-track and cross-track geoid gradients. Utilizing these methods, we developed a new global marine gravity model, SDUST2022GRA, from radar and laser altimeter data. Different weight determination methods were applied to each type of altimeter datum. The precision and spatial resolution of SDUST2022GRA were assessed against published altimeter-derived global gravity anomaly models (DTU17, V32.1, NSOAS22) and shipborne gravity measurements. SDUST2022GRA achieved a global precision of 4.43 mGal, representing an improvement of approximately 0.22 mGal over existing altimeter-derived models. In local coastal and high-latitude regions, SDUST2022GRA showed an enhancement of 0.16–0.24 mGal compared to the other models. The spatial resolution of SDUST2022GRA is approximately 20 km in certain regions, which is slightly superior to the other models. The percentage contribution of ICESat-2 to the improvement of the gravity anomaly model is 4.3 % in low- to mid-latitude regions by comparing SDUST2022GRA with ICESat-2 to SDUST2021GRA without ICESat-2, and this is increasing in coastal regions. These assessments suggest that SDUST2022GRA is a reliable global marine gravity anomaly model. The SDUST2022GRA data are freely available at https://doi.org/10.5281/zenodo.8337387 (Li et al., 2023).
Multiwavelength aerosol lidars at the Maïdo supersite, Réunion Island, France: instrument description, data processing chain, and quality assessment
Authors: Gantois Dominique , Payen Guillaume , Sicard Michaël , Duflot Valentin , Bègue Nelson , Marquestaut Nicolas , Portafaix Thierry , Godin-Beekmann Sophie , Hernandez Patrick , Golubic Eric 
Published: September 2024

Abstract. Understanding optical and radiative properties of aerosols and clouds is critical to reducing uncertainties in climate models. For over 10 years, the Observatory of Atmospheric Physics in Reunion (OPAR; 21.079° S, 55.383° E) has been operating three active lidar instruments, named lidar 1200 (Li1200), stratospheric ozone lidar (LiO3S), and tropospheric ozone lidar (LiO3T), providing time series of vertical profiles from 3 to 45 km of the aerosol extinction and backscatter coefficients at 355 and 532 nm as well as the linear depolarization ratio at 532 nm. This work provides a full technical description of the three systems, the details about the methods chosen for the signal preprocessing and processing, and an uncertainty analysis. About 1737 nighttime averaged profiles were manually screened to provide cloud-free and artifact-free profiles. Data processing consisted of Klett inversion to retrieve aerosol optical products from preprocessed files. The measurement frequency was lower during the wet season and the holiday periods. There is a good correlation between the Li1200 and LiO3S instruments in terms of stratospheric aerosol optical depth (AOD) at 355 nm (0.001–0.107; R=0.92±0.01) and with LiO3T in terms of Ångström exponent 355/532 (0.079–1.288; R=0.90±0.13). The lowest values of the averaged uncertainty in the aerosol backscatter coefficient for the three time series are 64.4 ± 31.6 % for LiO3S, 50.3 ± 29.0 % for Li1200, and 69.1 ± 42.7 % for LiO3T. These relative uncertainties are high for the three instruments because of the very low values of extinction and backscatter coefficients for background aerosols above Maïdo observatory. Uncertainty increases due to the signal-to-noise ratio (SNR) decrease above 25 km for LIO3S and Li1200 and above 20 km for LiO3T. The lidar ratio (LR) is responsible for an uncertainty increase below 18 km (10 km) for LiO3S and Li1200 (LiO3T). LiO3S is the most stable instrument at 355 nm due to fewer technical modifications and fewer misalignments. Li1200 is a valuable addition meant to fill in the gaps in the LiO3S time series at 355 nm or for specific case studies about the middle and low troposphere. Data described in this work are available at https://doi.org/10.26171/rwcm-q370 (Gantois et al., 2024).
AscDAMs: advanced SLAM-based channel detection and mapping system
Authors: Wang Tengfei , Lu Fucheng , Qin Jintao , Huang Taosheng , Kong Hui , Shen Ping 
Published: September 2024

Abstract. Obtaining high-resolution, accurate channel topography and deposit conditions has been a challenge for the study of channelized debris flow. Currently, widely used mapping technologies including satellite imaging and drone photogrammetry struggle to precisely observe channel interior conditions of long and deep mountainous gullies, particularly those in the Wenchuan earthquake region. SLAM is an emerging tech for 3D mapping; however, extremely rugged environment in long and deep gullies poses two major challenges even for the state-of-the-art SLAM: (1) atypical features and (2) violent swaying and oscillation of sensors. These issues result in large deviation and lots of noise for SLAM results. To improve SLAM mapping in such environments, we propose an advanced SLAM-based channel detection and mapping system, namely AscDAMs. It features three main enhancements to post-process SLAM results: (1) the digital orthophoto map-aided deviation correction algorithm greatly eliminates the systematic error; (2) the point cloud smoothing algorithm substantially diminishes noise; (3) the cross-section extraction algorithm enables the quantitative assessment of channel deposits and their changes. Two field experiments were conducted in Chutou gully, Wenchuan County in China in February and November 2023, representing observations before and after the rainy season. We demonstrate the capability of AscDAMs to greatly improve SLAM results, promoting SLAM for mapping the specially challenging environment. The proposed method compensates for the insufficiencies of existing technologies in detecting debris flow channel interiors including detailed channel morphology, erosion patterns, deposit distinction, volume estimation and change detection. It serves to enhance the study of full-scale debris flow mechanisms, long-term post-seismic evolution, and hazard assessment.
TEXT Poetry and Prose April 2020
Authors: Alexander Lucy , Baird Joshua , Billingham Craig , Durrant Judy , Kerrison Dean , Leggett Andrew , Maller Gershon , Nash Peter , Nonn Ann , Prendergast Julia , Wakelin Oliver , West Sean 
Published: September 2024

New creative works exploring creativity, or the nature and processes of writing. Julia Prendergast, Today is tomorrow Peter Nash, Gone Fishin’ Andrew Leggett, 3 poems Judy Durrant, 3 poems Joshua Baird, Brando Lucy Alexander, 2 poems Dean Kerrison, Green-eyed monster diary Gershon Maller, Palimpsest Ann Nonn, Dear Colleague Oliver Wakelin, Thalatta Craig Billingham, On the novel I did not write Sean West, 3 poems Julia Prendergast, Endgame
NOBREZA NEGRA EM BRIDGERTON: UMA ANÁLISE SOBRE CONSUMO DA IMAGEM NEGRA A PARTIR DE COMENTÁRIOS DE INTERNAUTAS
Authors: Silva Henrique Ferreira  da , Bonin Iara Tatiana 
Published: September 2024

A produção cultural Bridgerton, lançada pela Netflix em 2020, colocou em seu elenco atores negros em papéis nobres, constituindo um tipo de representação ambivalente que mobiliza e divide opiniões de internautas. À vista disso, o objetivo principal do presente artigo é discutir algumas formas de controle e de consumo da imagem do negro, tomando como materialidade empírica um conjunto de comentários feitos por internautas e postados no portal de notícias Mundo Negro, local virtual onde são mobilizadas pautas antirracistas. A metodologia envolve a análise cultural de 70 comentários, correspondentes à totalidade de postagens existentes abaixo de uma matéria jornalística sobre a série Bridgerton. A discussão respalda-se em conceitos como os de representação (Hall, 2016), imagens de controle (Collins, 2016) e negrofilia (Archer-Straw, 2000) e permite entender como os internautas reagem às posições construídas para os personagens negros na série.
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut
Authors: Carr Alex 
Published: September 2024

Clostridioides difficile colonizes up to 30-40% of community-dwelling adults without causing disease. C. difficile infections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance of C. difficile are still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances of C. difficile colonization susceptibility or resistance. MCMMs provide detailed mechanistic insights into the ecological interactions that govern C. difficile engraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinct C. difficile metabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 14,862 individuals from four independent cohorts. Finally, we show how MCMMs can predict personalized engraftment and C. difficile growth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalized C. difficile engraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to better understand personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.Link to OA publication: https://www.biorxiv.org/content/10.1101/2023.04.28.538771v2.abstract
Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics
Authors: Ghensi Paolo 
Published: September 2024

Dental implants are installed in an increasing number of patients. Mucositis and peri-implantitis are common microbial-biofilm-associated diseases affecting the tissues that surround the dental implant and are a major medical and socioeconomic burden. By metagenomic sequencing of the plaque microbiome in different peri-implant health and disease conditions (113 samples from 72 individuals), we found microbial signatures for peri-implantitis and mucositis and defined the peri-implantitis-related complex (PiRC) composed by the 7 most discriminative bacteria. The peri-implantitis microbiome is site specific as contralateral healthy sites resembled more the microbiome of healthy implants, while mucositis was specifically enriched for Fusobacterium nucleatum acting as a keystone colonizer. Microbiome-based machine learning showed high diagnostic and prognostic power for peri-implant diseases and strain-level profiling identified a previously uncharacterized subspecies of F. nucleatum to be particularly associated with disease. Altogether, we associated the plaque microbiome with peri-implant diseases and identified microbial signatures of disease severity. Link to the OA paper: https://www.nature.com/articles/s41522-020-00155-7
Using Combinatorial Transformation to produce Valuable Metabolites in Nicotiana tabacum
Authors: Kerr Stacey 
Published: September 2024

Cannabinoids such as cannabidiol (CBD) are important secondary metabolites produced mainly on the flowering parts of Cannabis sativa plants, which are known to have a multitude of human therapeutic values. Cannabis also produced over 120 different cannabinoids, with many therapeutics yet to be uncovered. However, cannabis cannot produce standardized amounts of cannabinoids. Different environmental factors such as light and water are known to affect both the amount and type of cannabinoids produced. My project overcomes this issue by introducing the cannabinoid metabolic pathway into a model plant species, *Nicotiana tabacum*, using combinatorial transformation. This involves introducing the set of genes required for metabolite production in a single bombardment, with independent plant lines being generated from subsequent regeneration. Results from this set of experiments show cannabinoid-producing transgenic tobacco lines, which is yet to be described in the literature. This study demonstrates the potential for *Nicotiana tabacum* to be used as a vessel for standardized secondary metabolite production.
Viroid-like colonists of human microbiomes
Authors: Zheludev Ivan 
Published: September 2024

Here, we describe the “Obelisks,” a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. “Obelisks” share several properties: (i) apparently circular RNA about 1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the “Oblins”. We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in about 7% of analysed stool metatranscriptomes (29/440) and in about 50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over 300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.Link to OA paper: https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Authors: Beghini Francesco 
Published: September 2024

Culture-independent analyses of microbial communities dramatically improved in the last decade, thanks to advances in methods for biological profiling via shotgun metagenomics and other molecular methods. This opens new opportunities for large-scale assembly efforts and the improvement of analysis tools with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated and improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes based on the largest set of reference sequences now available. MetaPhlAn 3 and HUMAnN 3 provides more accurate taxonomic and functional potential and activity profiles, respectively. These methods detected novel disease-microbiome links in CRC and IBD cohorts. Strain-level profiling of 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unravelled the phylogenetic and functional structure of the gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. Phylogenetic analysis with PhyloPhlAn 3 supports both genomic and metagenomic data, by assigning genomes from isolate sequencing or metagenomic assemblies to species-level genome bins defined on more than 230,000 publically available sequences. It also accurately reconstructs phylogenies at different resolutions (from strain-level to microbial tree-of-life) using maximally informative markers. The bioBakery 3 is open-source and includes documentation, training data, and cloud-deployable reproducible workflows to help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial communities. The ability to use metagenomic assemblies further help to study uncharacterized microbial species not represented by isolate genomes.article: https://elifesciences.org/articles/65088
A three strain postbiotic mix improves the immune system function after oral intake for 28-days
Authors: Castellana Jordi Cuñé 
Published: September 2024

Background: Dietary selenium complements are known to improve overall health and enhance different aspects of the immune response, participating in the function of the immune cells, cytokine secretion regulation of chronic inflammation and control of excessive immune responses. In this study, our objective was to evaluate whether a selenium-rich postbiotic composed of whole-cell Saccharomyces cerevisiae ABB S12, Kluyveromyces marxianus ABB S8 and Saccharomyces boulardii ABB S3 yeast strains, can act as provider of selenium to enhance the function of the human immune system after oral intake.
Methods and findings: A total of 15 volunteers were enrolled in a 28-day clinical study in which they complemented their normal diets with a daily dose of a novel selenium food supplement, “postbiotic immune”. Selenium levels in plasma were quantified by ELISA (Enzyme Linked Immuno Sorbent Assay), and the proliferation and activation of different subsets of lymphocytes isolated from PBMC’s (Peripheral Blood Mononuclear Cells) were assessed by flow cytometry using different cell markers. At the end of the study, we observed a higher proliferative capacity of total lymphocytes and specifically, of CD16+ lymphocytes (natural killer cells), upon stimulation with the CD3 and CD28 antibodies mimicking cell activation in vitro. Interestingly, we did not observe an increase in the activation of the lymphocyte subsets CD4+ (T helper cells) but CD16+, indicating that that there was a specific activation of natural killer cells.
Conclusions: Altogether, our results suggest that orally ingested ”Postbiotic immune” primes the human immune system to elicit a faster and more efficient immune response through the specific activation of natural killer cells.Link to publication:
https://nutraceuticals.imedpub.com/a-three-strain-postbiotic-mix-improves-the-immune-system-function-after-oral-intake-for-28days.php?aid=52017
Human gut microbiome-dependent energy-extraction
Authors: Roager Henrik 
Published: September 2024

More than 15 years ago, it was hypothesised that the gut microbiota could causally affect weight gain due to the gut microbiome’s capacity to extract energy from the diet. Yet, evidence linking microbiome-dependent energy harvest to particular human gut microbiome compositions have been lacking. In this recently published study, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and structure. We found opposite of what we expected that stool energy density was positively associated with intestinal transit time. Furthermore, individuals with a Bacteroides enterotype (B-type) had significantly lower energy left in faeces (per gram dried faeces) compared to individuals with a Ruminococcaecea enterotype (R-type). The B-type individuals had lower alpha-diversity and faster intestinal transit time, but also a significantly higher body weight compared to the R-type individuals. Furthermore, markers of proteolytic fermentation were increased in the R-type compared to the B-type. Together, this could suggest that human gut microbiome-dependent energy extraction is diversified according to intestinal transit time and gut microbiome ecosystem variations as reflected by enterotypes. While the causalities remain to be established, the observations are intriguing and could provide new dietary strategies in body weight management. Link to OA paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01418-5
Time of Sample Collection Critical for Microbiome Replicability
Authors: Allaband Celeste 
Published: September 2024

Although many aspects of microbiome studies have been standardized to improve experimental replicability, none account for how the daily diurnal fluctuations in the gut lumen cause dynamic changes in 16S amplicon sequencing. Here we show that sample collection time affects the conclusions drawn from microbiome studies and are larger than the effect size of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups are unique to each experiment. Sample collection times as short as only four hours apart lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. Without looking at other data, the impact on other fields is unknown but potentially significant.Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.10.26.513817v1