bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bridging the gap in fishing effort mapping: a spatially-explicit fisheries dataset for Campanian MPAs, Italy
Authors: Lattanzi Pamela , Pulcinella Jacopo , Battaglia Pietro , Di Cintio Antonio , Ferrà Carmen , Di Franco Antonio , Tassetti Anna Nora 
Published: January 2024

AbstractRecent technological advancements have facilitated the extensive collection of movement data from large-scale fishing vessels, yet a significant data gap remains for small-scale fisheries. This gap hinders the development of consistent exploitation patterns and meeting the information needs for marine spatial planning in fisheries management. This challenge is specifically addressed in the Campania region of Italy, where several Marine Protected Areas support biodiversity conservation and fisheries management. The authors have created a spatially-explicit dataset that encompasses both large-scale (vessels exceeding 12 meters in length) and small-scale (below 12 meters) fishing efforts. This dataset (available at https://doi.org/10.6084/m9.figshare.23592006) is derived from vessel tracking data and participatory mapping. It offers insights into potential conflicts between different fishing segments and their interactions with priority species and habitats. The data can assist researchers and coastal management stakeholders in formulating policies that reduce resource competition and promote ecosystem-based fisheries management. Furthermore, the provided mapping approach is adaptable for other regions and decision-making frameworks, as we are committed to sharing the tools and techniques we employed.
De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus)
Authors: Wang Xinrui , Zhang Lili , Yao Gang , Wang Xiangfeng , Yi Shu , Meng Tan , Meng Dian , Chen Weikai , Guo Li 
Published: January 2024

AbstractChinese motherwort (Leonurus japonicus), a member of Lamiaceae family, is a commonly used medicinal herb for treating obstetrical and gynecological diseases, producing over 280 officinal natural products. Due to limited genomic resources, little progress has been made in deciphering the biosynthetic pathway of valuable natural products in L. japonicus. Here, we de novo assembled the L. japonicus genome using high-coverage ONT long reads and Hi-C reads. The chromosome-level genome assembly contained ten chromosomes representing 99.29% of 489.34 Mb genomic sequence with a contig and scaffold N50 of 7.27 Mb and 50.86 Mb, respectively. Genome validations revealed BUSCO and LAI score of 99.2% and 21.99, respectively, suggesting high quality of genome assembly. Using transcriptomic data from various tissues, 22,531 protein-coding genes were annotated. Phylogenomic analysis of 13 angiosperm plants suggested L. japonicus had 58 expanded gene families functionally enriched in specialized metabolism such as diterpenoid biosynthesis. The genome assembly, annotation, and sequencing data provide resources for the elucidation of biosynthetic pathways behind natural products of pharmaceutical applications in L. japonicus.
GDF15 as a potential biomarker to distinguish fibrotic from non-fibrotic hypersensitivity pneumonitis
Authors: Alarcon-Dionet A. , Ruiz A. , Chavez-Galan L. , Buendia-Roldan I. , Selman M. 
Published: January 2024

AbstractHypersensitivity Pneumonitis (HP) is an immune-mediated interstitial lung disease (ILD) characterized by fibrotic HP (fHP) or non-fibrotic HP (non-fHP). Fibrosis is associated with poor prognosis, emphasizing the need for biomarkers to distinguish fHP from non-fHP. This study aimed to determine the plasma levels of GDF15 in HP patients and assess its association with lung function and phenotype classification. GDF15 levels were quantified by ELISA in HP (n = 64), idiopathic pulmonary fibrosis (n = 54), and healthy control (n = 128) groups. Clinical, demographic, and functional data were obtained from medical records. High-resolution chest CT scans were used to classify HP patients into fHP and non-fHP groups. In addition, receiver operating characteristic analysis was performed to determine the cut-off point, sensitivity, and specificity. Our results revealed significantly elevated GDF15 levels in fHP compared to non-fHP (2539 ± 821 pg/ml versus 1783 ± 801 pg/ml; p = 0.009). The estimated cut-off point for plasma GDF15 levels to distinguish fHP from non-fHP was 2193.4 pg/ml (AUC 0.75). These findings suggest that GDF15 may serve as a valuable biomarker for differentiating between fHP and non-fHP, potentially indicating its involvement in lung fibrosis development in HP.
Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance
Authors: Bambi Marina , Galla Giulio , Donati Claudio , Rovero Francesco , Hauffe Heidi C. , Barelli Claudia 
Published: January 2024

AbstractAlthough male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi (gut microbiota) in relation to habitat type has not been fully examined. To understand whether the combination of sex and habitat affects gut microbiota variation, we analyzed 40 fecal samples of wild yellow baboons (Papio cynocephalus) living in contrasting habitat types (intact, well-protected vs. fragmented, less protected forests) in the Udzungwa Mountains of Tanzania. Sex determination was performed using the marker genes SRY (Sex-determining Region Y) and DDX3X-DDX3Y (DEAD-Box Helicase 3). Samples were attributed to 34 individuals (19 females and 15 males) belonging to five social groups. Combining the results of sex determination with two amplicon sequencing datasets on bacterial (V1–V3 region of the 16S rRNA gene) and fungal (ITS2) gut communities, we found that overall, baboon females had a significantly higher gut bacterial richness compared to males. Beta diversity estimates indicated that bacterial composition was significantly different between males and females, and this was true for individuals from both well- and less protected forests. Our results highlight the combined role of sex and habitat type in shaping variation in gut microbial communities in wild non-human primates.
Kinetic study of membrane protein interactions: from three to two dimensions
Authors: Adrien Vladimir , Reffay Myriam , Taulier Nicolas , Verchère Alice , Monlezun Laura , Picard Martin , Ducruix Arnaud , Broutin Isabelle , Pincet Frédéric , Urbach Wladimir 
Published: January 2024

AbstractMolecular interactions are contingent upon the system’s dimensionality. Notably, comprehending the impact of dimensionality on protein–protein interactions holds paramount importance in foreseeing protein behaviour across diverse scenarios, encompassing both solution and membrane environments. Here, we unravel interactions among membrane proteins across various dimensionalities by quantifying their binding rates through fluorescence recovery experiments. Our findings are presented through the examination of two protein systems: streptavidin–biotin and a protein complex constituting a bacterial efflux pump. We present here an original approach for gauging a two-dimensional binding constant between membrane proteins embedded in two opposite membranes. The quotient of protein binding rates in solution and on the membrane represents a metric denoting the exploration distance of the interacting sites—a novel interpretation.
Understanding the molecular mechanism of pathogenic variants of BIR2 domain in XIAP-deficient inflammatory bowel disease
Authors: Lee Juhwan , Sim Kyoung Mi , Kang Mooseok , Oh Hyun Ju , Choi Ho Jung , Kim Yeong Eun , Pack Chan-Gi , Kim Kyunggon , Kim Kyung Mo , Oh Seak Hee , Kim Inki , Chang Iksoo 
Published: January 2024

AbstractX-linked inhibitor of apoptosis protein (XIAP) deficiency causes refractory inflammatory bowel disease. The XIAP protein plays a pivotal role in the pro-inflammatory response through the nucleotide-binding oligomerization domain-containing signaling pathway that is important in mucosal homeostasis. We analyzed the molecular mechanism of non-synonymous pathogenic variants (PVs) of XIAP BIR2 domain. We generated N-terminally green fluorescent protein-tagged XIAP constructs of representative non-synonymous PVs. Co-immunoprecipitation and fluorescence cross-correlation spectroscopy showed that wild-type XIAP and RIP2 preferentially interacted in live cells, whereas all non-synonymous PV XIAPs failed to interact properly with RIP2. Structural analysis showed that various structural changes by mutations, such as hydrophobic core collapse, Zn-finger loss, and spatial rearrangement, destabilized the two loop structures (174–182 and 205–215) that critically interact with RIP2. Subsequently, it caused a failure of RIP2 ubiquitination and loss of protein deficiency by the auto-ubiquitination of all XIAP mutants. These findings could enhance our understanding of the role of XIAP mutations in XIAP-deficient inflammatory bowel disease and may benefit future therapeutic strategies.
Tumor-specific migration routes of xenotransplanted human glioblastoma cells in mouse brain
Authors: Gupta Rajesh Kumar , Niklasson Mia , Bergström Tobias , Segerman Anna , Betsholtz Christer , Westermark Bengt 
Published: January 2024

AbstractThe migration of neural progenitor cells (NPCs) to their final destination during development follows well-defined pathways, such as along blood vessels. Cells originating from the highly malignant tumor glioblastoma (GBM) seem to exploit similar routes for infiltrating the brain parenchyma. In this report, we have examined the migration of GBM cells using three-dimensional high-resolution confocal microscopy in brain tumors derived from eight different human GBM cell lines xenografted into immunodeficient mice. The primary invasion routes identified were long-distance migration along white matter tracts and local migration along blood vessels. We found that GBM cells in the majority of tumors (6 out of 8) did not exhibit association with blood vessels. These tumors, derived from low lamin A/C expressing GBM cells, were comparatively highly diffusive and invasive. Conversely, in 2 out of 8 tumors, we noted perivascular invasion and displacement of astrocyte end-feet. These tumors exhibited less diffusive migration, grew as solid tumors, and were distinguished by elevated expression of lamin A/C. We conclude that the migration pattern of glioblastoma is distinctly tumor cell-specific. Furthermore, the ability to invade the confined spaces within white matter tracts may necessitate low expression of lamin A/C, contributing to increased nuclear plasticity. This study highlights the role of GBM heterogeneity in driving the aggressive growth of glioblastoma.
Wing geometric morphometrics and COI barcoding of Culex pipiens subgroup in the Republic of Korea
Authors: Jeon Jiseung , Lee Dong Yeol , Jo Yewon , Ryu Jihun , Kim Eunjeong , Choi Kwang Shik 
Published: January 2024

AbstractTwo members of theCulex pipienssubgroup,Culex pallensandCulex pipiensf.molestus, are known to occur in the Republic of Korea (ROK). These species exhibit morphologically similar features and are challenging to distinguish below the species level. Therefore, this study utilized wing geometric morphometrics (GM) on the right wing of theCulex pipienssubgroup, alongside sequencing of the cytochromecoxidase subunit I (COI) region. Mosquitoes were collected from 11 locations between June and October (2020–2022) to minimize regional and seasonal variations. Additionally,Culex pipiensf.pipiens, which is not native to the ROK, was included in the analysis.Culex tritaeniorhynchus,Aedes albopictus, andAnopheles sinensis, the primary vectors in the ROK, were used as outgroups for comparison. All three taxa in theCulex pipienssubgroup could be identified with an 82.4%–97.0% accuracy using GM. However, a comparison of theCOIregions of theCulex pipienssubgroup revealed no clear differences between the taxa. These data can be used for accurate identification, contributing to effective mosquito control, in addition to providing a foundation for evolutionary and ecological studies on wing shape differences.
Detection ranges of forest bird vocalisations: guidelines for passive acoustic monitoring
Authors: Winiarska Dominika , Szymański Paweł , Osiejuk Tomasz S. 
Published: January 2024

AbstractPassive acoustic monitoring has proven to have many advantages for monitoring efforts and research activities. However, there are considerations to be taken into account regarding the placement of autonomous sound recorders. Detection ranges differ among species and in response to variable conditions such as weather or the location of vocalising animals. It is thus important to the success of a research project to understand, with a certain degree of confidence, the distances at which birds might be detected. In two types of forests in Poland, we played back the vocalisations of 31 species of European forest birds exemplifying different singing characteristics. Based on recordings obtained along a 500-m transect, we estimated the probability of detection and maximum detection distance of each vocalisation. We broadcasted the recording at three heights of singing and repeated playbacks three times during the breeding season to evaluate the effect of vegetation growth. Our results revealed that environmental and meteorological factors had a significant influence on both detection probability and maximum detection distances. This work provides comprehensive measurements of detection distance for 31 bird species and can be used to plan passive acoustic monitoring research in Europe, taking into account species traits and individual characteristics of the study area.
Uncovering hidden cancer self-dependencies through analysis of shRNA-level dependency scores
Authors: Toghrayee Zohreh , Montazeri Hesam 
Published: January 2024

AbstractLarge-scale short hairpin RNA (shRNA) screens on well-characterized human cancer cell lines have been widely used to identify novel cancer dependencies. However, the off-target effects of shRNA reagents pose a significant challenge in the analysis of these screens. To mitigate these off-target effects, various approaches have been proposed that aggregate different shRNA viability scores targeting a gene into a single gene-level viability score. Most computational methods for discovering cancer dependencies rely on these gene-level scores. In this paper, we propose a computational method, named NBDep, to find cancer self-dependencies by directly analyzing shRNA-level dependency scores instead of gene-level scores. The NBDep algorithm begins by removing known batch effects of the shRNAs and selecting a subset of concordant shRNAs for each gene. It then uses negative binomial random effects models to statistically assess the dependency between genetic alterations and the viabilities of cell lines by incorporating all shRNA dependency scores of each gene into the model. We applied NBDep to the shRNA dependency scores available at Project DRIVE, which covers 26 different types of cancer. The proposed method identified more well-known and putative cancer genes compared to alternative gene-level approaches in pan-cancer and cancer-specific analyses. Additionally, we demonstrated that NBDep controls type-I error and outperforms statistical tests based on gene-level scores in simulation studies.
Establishment of a forward primers-superposed amplification analysis for accurate aspirin pharmacogenomic measurement
Authors: Li Chun-Yan , Yang Ping , Zheng Jie , Zhang Jing , Liu Yi-Qing , Liu Xiao-Quan , Hu Yue , Lan Wen-Jun 
Published: January 2024

AbstractGenotyping of gDNA rs12041331 (PEAR1), rs6065 (GP1BA), and rs730012 (LTC4S) can provide systematic guidance on the use of aspirin. However, an accurate, reliable and economical approach to simultaneous detection of the above single nucleotide polymorphisms (SNPs) is not reported. Herein, we designed and substantiated an allele-specific (AS) forward primer-superposed amplification analysis for measurement of the SNPs in PEAR1, GP1BA and LTC4S genes, in which the values of ∆Cq (differences in threshold cycles between the wild-type forward primer-based assay and the mutated-type forward primer-based assay) were employed to decide genotype. Mismatch AS forward primers were screened with the singleplex amplification analysis. Moreover, Cq extension optimized by AS forward primer superposition was observed in the selected forward primer-based triplex analysis. Further, robustness assessment of the triplex analysis showed the amplification efficiency ranging from 0.9 to 1.1. Precision test demonstrated the coefficient of variation of less than 2%. And the detective results of 189 DNA samples was completely concordant with that of commercial Sanger sequencing. In summary, we developed a simple, accurate and economical approach to genotyping of rs12041331 (PEAR1), rs6065 (GP1BA) and rs730012 (LTC4S) to provide a valuable pharmacogenomics tool for guidance of aspirin delivery.
Role of Madden–Julian Oscillation in predicting the 2020 East Asian summer precipitation in subseasonal-to-seasonal models
Authors: Wie Jieun , Kang Jinhee , Moon Byung-Kwon 
Published: January 2024

AbstractThe 2020 summer monsoon season in East Asia was unusually long and intense, and the Madden–Julian Oscillation (MJO) has been proposed as an underlying reason. This study analyzes the role of the MJO in the 2020 East Asian precipitation forecasts of the subseasonal-to-seasonal (S2S) model. The S2S models underestimated the cumulative precipitation over East Asia, and the models with good forecast performance yielded a distinct precipitation band over East Asia and a western pacific subtropical high (WPSH) during the analysis period. East Asian precipitation forecast performance was more closely related to the location of the center than the strength of the WPSH, with precipitation increasing with a decrease in the latitude at the center. MJO Phases 1–3 activation intensified the WPSH and shifted the center of WPSH to lower latitudes. Our results confirm that the strong East Asian precipitation in summer 2020 was partly due to changes in the characteristics of the MJO and indicate the importance of accurately estimating the MJO-WPSH coupling for reliable East Asian precipitation forecasts.
Spatial proteomics reveals phenotypic and functional differences in T cell and macrophage subsets during villitis of unknown etiology
Authors: Lothert Petra K. , Fedyshyn Bohdana , Girard Sylvie , Chakraborty Rana , Norgan Andrew P. , Enninga Elizabeth Ann L. 
Published: January 2024

AbstractVillitis of unknown etiology (VUE) is a prevalent inflammatory pathology of the placenta characterized by infiltration of maternal T cells and accumulation of fetal macrophages into chorionic villi. VUE is associated with a variety of adverse clinical outcomes, including fetal growth restriction and fetal demise. Evaluation of the phenotypic and functional differences between two immune cell types associated with this pathology, namely T cells and macrophages, was completed to gain a deeper understanding of the immuno-pathogenesis of VUE. GeoMx Digital Spatial Profiling was performed on placental tissue from 4 high grade VUE cases and 4 controls with no underlying pathology. Placental tissues were fluorescently labeled with CD3 and CD68 antibodies and oligo-conjugated antibodies against 48 protein targets. Overall, T cells in VUE exhibited upregulated markers of activation, memory, and antigen experience compared to controls and were altered based on placental location (villi vs. decidua). Additionally, villous macrophages in VUE upregulated costimulatory and major histocompatibility complex class I and II molecules compared to controls and macrophage subtypes in the decidua. Data herein provides new mechanistic insights into T cell and macrophage biology in VUE which contribute to this abnormal immune response to pregnancy.
Simulated microgravity facilitates stomatal ingression by Salmonella in lettuce and suppresses a biocontrol agent
Authors: Totsline Noah , Kniel Kalmia E. , Sabagyanam Chandran , Bais Harsh P. 
Published: January 2024

AbstractAs human spaceflight increases in duration, cultivation of crops in spaceflight is crucial to protecting human health under microgravity and elevated oxidative stress. Foodborne pathogens (e.g., Salmonella enterica) carried by leafy green vegetables are a significant cause of human disease. Our previous work showed that Salmonella enterica serovar Typhimurium suppresses defensive closure of foliar stomata in lettuce (Lactuca sativa L.) to ingress interior tissues of leaves. While there are no reported occurrences of foodborne disease in spaceflight to date, known foodborne pathogens persist aboard the International Space Station and space-grown lettuce has been colonized by a diverse microbiome including bacterial genera known to contain human pathogens. Interactions between leafy green vegetables and human bacterial pathogens under microgravity conditions present in spaceflight are unknown. Additionally, stomatal dynamics under microgravity conditions need further elucidation. Here, we employ a slow-rotating 2-D clinostat to simulate microgravity upon in-vitro lettuce plants following a foliar inoculation with S. enterica Typhimurium and use confocal microscopy to measure stomatal width in fixed leaf tissue. Our results reveal significant differences in average stomatal aperture width between an unrotated vertical control, plants rotated at 2 revolutions per minute (2 RPM), and 4 RPM, with and without the presence of S. typhimurium. Interestingly, we found stomatal aperture width in the presence of S. typhimurium to be increased under rotation as compared to unrotated inoculated plants. Using confocal Z-stacking, we observed greater average depth of stomatal ingression by S. typhimurium in lettuce under rotation at 4 RPM compared to unrotated and inoculated plants, along with greater in planta populations of S. typhimurium in lettuce rotated at 4 RPM using serial dilution plating of homogenized surface sterilized leaves. Given these findings, we tested the ability of the plant growth-promoting rhizobacteria (PGPR) Bacillus subtilis strain UD1022 to transiently restrict stomatal apertures of lettuce both alone and co-inoculated with S. typhimurium under rotated and unrotated conditions as a means of potentially reducing stomatal ingression by S. typhimurium under simulated microgravity. Surprisingly, rotation at 4 RPM strongly inhibited the ability of UD1022 alone to restrict stomatal apertures and attenuated its efficacy as a biocontrol following co-inoculation with S. typhimurium. Our results highlight potential spaceflight food safety issues unique to production of crops in microgravity conditions and suggest microgravity may dramatically reduce the ability of PGPRs to restrict stomatal apertures.