bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using 18F-NOS PET Imaging to Measure Pulmonary Inflammation in Electronic and Combustible Cigarette Users: A Pilot Study
Authors: Wetherill Reagan R. , Doot Robert K. , Young Anthony J. , Lee Hsiaoju , Schubert Erin K. , Wiers Corinde E. , Leone Frank T. , Mach Robert H. , Kranzler Henry R. , Dubroff Jacob G. 
Published: June 2022

AbstractElectronic cigarette (EC) use has increased dramatically, particularly among adolescents and young adults, which, like cigarette use, can cause inflammation of the lungs and increase the risk of lung disease.MethodsIn this preliminary study, we used positron emission tomography with 18F-6-(1/2)(2-fluoro-propyl)-4-methylpyridin-2-amine (18F-NOS) to quantify inflammation of the lungs in vivo in three age- and sex-matched groups: (1) 5 daily EC users, (2) 5 daily cigarette smokers, and (3) 5 never smoke/vape controls.ResultsEC users showed greater 18F-NOS non-displaceable binding potential (BPND) than cigarette smokers (p = 0.03) and never smoke/vape controls (p = 0.01); whereas BPND in cigarette smokers did not differ from controls (p > 0.1). 18F-NOS lung tissue delivery (K1) and iNOS distribution volume (VT) did not significantly differ between groups. Although there were no group differences in the concentration of the peripheral inflammatory markers TNF-α, IL-6 or IL-8, 18F-NOS BPND significantly correlated with the proinflammatory cytokine TNF-α (r = 0.87, p = 0.05) in EC users. Additionally, when EC users and cigarette smokers were pooled together, vaping episodes/cigarettes per day correlated with IL-6 levels (r = 0.86, p = 0.006).ConclusionTo our knowledge, this is the first PET imaging study to compare lung inflammation between EC and cigarette users in vivo. We found preliminary evidence EC users had greater pulmonary inflammation than cigarette smokers and never smoke/vape controls, with a positive association between pulmonary and peripheral measures of inflammation.
eccDNA purification, full-length sequencing, and genomic mapping
Authors: Wang Yuangao , Wang Meng , Zhang Yi 
Published: June 2022

AbstractExtrachromosomal circular DNA (eccDNA) has been discovered for more than half a century1. However, its biogenesis and function have just begun to be elucidated. One hurdle that prevented our understanding of eccDNA is the difficulty in obtaining pure eccDNA from cells. The current eccDNA purification methods mainly rely on exonuclease digestion after alkaline lysis. Due to its low abundance and heterogeneity in size, the current eccDNA purification methods are not efficient in obtaining pure eccDNA. Here, we describe a new 3-step eccDNA purification (3SEP) procedure by adding a new step that allows circular, but not linear, DNA that escaped from exonuclease digestion, bound to silica beads in solution A. Our method allows eccDNA purification with high purity and reproducibility. Additionally, we developed a full-length sequencing and genomic mapping method by combining rolling cycle amplification (RCA) with Nanopore sequencing, through which the consensus sequence of multiple tandem copies of eccDNA contained within the debranched RCA product is derived and mapped to its genomic origin. Collectively, our protocol will facilitate eccDNA identification, characterization, and has the potential for diagnostic and clinic applications.
A pangenome analysis pipeline (PSVCP) provides insights into rice functional gene identification
Authors: Wang Jian , Yang Wu , Zhang Shaohong , Hu Haifei , Yuan Yuxuan , Dong Jingfang , Chen Luo , Ma Yamei , Yang Tifeng , Zhou Lian , Chen Jiansong , Liu Bin , Li Chengdao , Edwards David , Zhao Junliang 
Published: June 2022

AbstractBackgroundA pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, there is a lack of bioinformatics analysis tools for graph format genomes.ResultsTo overcome this problem, we have developed a novel pangenome construction strategy and a downstream pangenome analysis pipeline that captures position information while maintaining a linearized layout. We applied this strategy to construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome reference. Our results provide insights into rice population structure and genomic diversity. Applying the pangenome for PAV-based GWAS analysis can identify causal structural variations for rice grain weight and plant height, while SNP-based GWAS can only identify approximate genomic locations. Additionally, a new locus (qPH8-1) was found to be associated with plant height on chromosome 8 that could not be detected using the SNP-based GWAS.ConclusionsOur results demonstrate that the pangenome constructed by our pipeline combined with PAV-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and associated genome sequence data provide valuable genomic resources for future rice crop improvement.
Label-free, fast, 2-photon volume imaging of the structural organization of peripheral neurons and glia in the enteric ganglia
Authors: Hazart Doriane , Delhomme Brigitte , Oheim Martin , Ricard Clément 
Published: June 2022

ABSTRACTThe enteric nervous system (ENS), sometimes considered as a ‘second brain’ due to its large autonomy from central circuits is made of interconnected plexuses organized in a mesh-like network lining the gastrointestinal tract. Originally described as a leading actor of the regulation of digestion, bowel advance and intestinal secretion, its implication in various neuropathologies has recently been demonstrated. However, with few exceptions, its morphology and functions have been studied on thin sections of the intestinal wall or in dissected explants. Due to its intricate morphology, precious information on its three-dimensional (3-D) architecture and connectivity is often lost. In this context, we have developed a fast, label-free 3-D imaging method of the ENS, based on intrinsic signals of the tissue. We adapted a fast tissue-clearing protocol based on a high refractive-index aqueous solution, and then characterized the autofluorescence signals arising from the various cellular and sub-cellular components of the ENS. Immunofluorescence and spectral recordings complete this characterization. Finally, we demonstrate the fast acquisition of detailed 3-D image stacks of unlabeled mouse intestine, across the whole intestinal wall and including both the myenteric and submucosal enteric nervous plexuses using a new spinning-disk two-photon microscope. The combination of fast clearing (less than 15min for 73 % transparency), autofluorescence imaging and rapid volumetric imaging (less than a minute for the acquisition of s z-stack of 100 planes (150*150 µm) at 300-nm spatial resolution) paves the way for new applications in fundamental and clinical research.
Statistical Population Reconstruction of Moose (Alces alces) in Northeastern Minnesota using Integrated Population Models
Authors: Severud William J. , Berg Sergey S. , Ernst Connor A. , DelGiudice Glenn D. , Moore Seth A. , Windels Steve K. , Moen Ron A. , Isaac Edmund J. , Wolf Tiffany M. 
Published: June 2022

AbstractGiven recent and abrupt declines in the abundance of moose (Alces alces) throughout parts of Minnesota, accurately estimating statewide population trends and demographic parameters is a high priority for their continued management and conservation. Statistical population reconstruction using integrated population models provides a flexible framework for combining information from multiple studies across the state to produce robust estimates of population abundance, recruitment, and survival. We used this framework to combine aerial survey data and survival data from telemetry studies to recreate trends and demographics of moose in northeastern Minnesota, USA, from 2005 to 2020. Statistical population reconstruction confirmed the sharp decline in abundance from an estimated 7,841 (90% CI = 6,702–8,933) in 2009 to 3,386 (90% CI = 2,681–4,243) animals in 2013, but also indicated that abundance has remained relatively stable since then, except for a slight decline to 3,163 (90% CI = 2,403– 3,718) in 2020. Subsequent stochastic projection of the population from 2021 to 2030 suggests that this modest decline will continue for the next ten years. Both annual adult survival and per-capita recruitment (number of calves that survived to 1 year per adult female alive during the previous year) decreased substantially in years 2005 and 2019, from 0.902 (SE = 0.043) to 0.689 (SE = 0.061) and from 0.386 (SE = 0.030) to 0.303 (SE = 0.051), respectively. Sensitivity analysis revealed that moose abundance was more sensitive to fluctuations in adult survival than recruitment, leading us to conclude that the steep decline in 2013 was driven primarily by decreasing adult survival. Our analysis demonstrates the potential utility of using statistical population reconstruction to monitor moose population trends and to identify population declines more quickly. Future studies should focus on providing better estimates of per-capita recruitment, using pregnancy rates and calf survival, which can then be incorporated into reconstruction models to help improve estimates of population change through time.
Fatty acid binding protein 1 and fatty acid synthetase overexpression have differential effects on collagen III and cross-linking in Zongdihua pig tissues
Authors: Yang Rong , Zhou Di , Yan Zhihong , Zhao Zhonghai , Wang Yan , Li Jun , Ren Liqun , Xie Lingling , Wang Xin 
Published: June 2022

AbstractThe purpose of this study was to determine whether FABP1 and FAS regulate expression of collagen and its crosslinking via lysyl oxidase in Zongdihua pigs. We wished to identify processes affecting meat quality using molecular genetics to provide a basis for breeding improvement of these animals. We measured expression levels of FABP1 and related genes using qRT-PCR in longissimus dorsi muscle and subcutaneous adipose tissues. Primary adipocytes from fat tissues were isolated and FABP1 and FAS were overexpressed from recombinant plasmids. Our sequence analysis of the cloned genes indicated that FABP1 gene encodes a hydrophobic protein of 128 amino acids and contained 12 predicted phosphorylation sites and no transmembrane region. FAS encodes 333 amino acid hydrophobic protein containing with 26 phosphorylation sites and 0 transmembrane regions. The basal levels of FABP1 and FAS in pig tissues expression were 3 −3.5-fold higher in subcutaneous fat compared with muscle (P < 0.01). Recombinant expression plasmids were successfully transfected into the cloned preadipocytes and (a) overexpression of FAS resulted in significantly increased expression of COL3A1 gene (P < 0.05) and significantly inhibited lysyl oxidase LOX expression (P < 0.01); (b) overexpression of FABP1 significantly increased COL3A1 expression (P < 0.01) and significantly inhibited LOX expression (P < 0.05) and significantly reduced lysyl oxidase activity (P < 0.01). Therefore, enhancing FABP1 expression increases collagen accumulation and this preliminarily suggests that FAS and FABP1 can serve as fat-related candidate genes providing a theoretical basis for the study of fat deposition in Zongdihua pigs.
Sampling strategies and pre-pandemic surveillance gaps for bat coronaviruses
Authors: Cohen Lily E. , Fagre Anna C. , Chen Binqi , Carlson Colin J. , Becker Daniel J. 
Published: June 2022

AbstractThe emergence of SARS-CoV-2, and the challenge of pinpointing its ecological and evolutionary context, has highlighted the importance of evidence-based strategies for monitoring viral dynamics in bat reservoir hosts. Here, we compiled the results of 93,877 samples collected from bats across 111 studies between 1996 and 2018, and used these to develop an unprecedented open database, with over 2,400 estimates of coronavirus infection prevalence or seroprevalence at the finest methodological, spatiotemporal, and phylogenetic level of detail possible from public records. These data revealed a high degree of heterogeneity in viral prevalence, reflecting both real spatiotemporal variation in viral dynamics and the effect of variation in sampling design. Phylogenetically controlled meta-analysis revealed that the most significant determinant of successful viral detection was repeat sampling (i.e., returning to the same site multiple times); however, fewer than one in five studies longitudinally collected and reported data. Viral detection was also more successful in some seasons and from certain tissues, but was not improved by the use of euthanasia, indicating that viral detection may not be improved by terminal sampling. Finally, we found that prior to the pandemic, sampling effort was highly concentrated in ways that reflected concerns about zoonotic risk, leaving several broad geographic regions (e.g., South Asia, Latin America and the Caribbean, and most of Sub-Saharan Africa) and bat subfamilies (e.g., Stenodermatinae and Pteropodinae) measurably undersampled. These gaps constitute a notable vulnerability for global health security and will likely be a future barrier to contextualizing the origin of novel zoonotic coronaviruses.
Duodenal alpha-Synuclein pathology and enteric gliosis in advanced Parkinson’s Disease patients
Authors: Emmi Aron , Sandre Michele , Russo Francesco Paolo , Tombesi Giulia , Garrì Federica , Campagnolo Marta , Carecchio Miryam , Biundo Roberta , Spolverato Gaya , Macchi Veronica , Savarino Edoardo , Farinati Fabio , Parchi Piero , Porzionato Andrea , Bubacco Luigi , De Caro Raffaele , Kovacs Gabor G , Antonini Angelo 
Published: June 2022

ABSTRACTBackgroundThe role of the gut-brain axis has been recently highlighted as a major contributor to Parkinson’s Disease (PD) physiopathology, with numerous studies investigating bidirectional transmission of pathological protein aggregates, such as α-Synuclein (αSyn), in the context of neurodegenerative disease. However, little and often conflictual evidence is available from human studies due to patient heterogeneity, sampling variability, and the employment of antibodies with affinity for different αSyn epitopes.ObjectivesWe aimed to investigate the enteric nervous system (ENS) in PD by characterizing αSyn alterations and glial responses in duodenum biopsies of PD patients by employing topography-specific sampling and conformation-specific αSyn antibodies.Methods18 Patients with symptomatic PD who underwent Duodopa Percutaneous Endoscopic Gastrostomy and Jejunal Tube (PEG-J) procedure, as well as 18 age- and -sex-matched Healthy Control subjects undergoing routine diagnostic endoscopy, were included in the study. A mean of 4 duodenal wall biopsies were sampled from each patient. Immunohistochemistry was performed for anti-aggregated αSyn (5G4) and GFAP antibodies. Morphometrical-semi-quantitative analysis was performed to characterize αSyn-5G4+ and GFAP+ density and size.ResultsElevated immunoreactivity for aggregated α-Syn was identified in all biopsies of PD patients compared to controls. αSyn-5G4+ colocalized with neuronal marker β-III-tubulin. Evaluation of enteric glia cells revealed an increased size and density when compared with controls, suggesting reactive gliosis.ConclusionsDuodenal biopsy may represent a feasible and reliable tool for characterizing PD pathology in the GI tract and discerning patients from controls. Future studies are required to confirm these findings in a prodromal or early PD phase.
Targeting H3K4 methylation as a novel therapeutic strategy against tumor infiltration and nuclear changes of acute lymphoblastic leukemia cells
Authors: González-Novo Raquel , de Lope-Planelles Ana , González-Murillo África , Madrazo Elena , Acitores David , de Lacoba Mario García , Ramírez Manuel , Redondo-Muñoz Javier 
Published: June 2022

SummaryAcute lymphoblastic leukemia (ALL) is the most common pediatric cancer, and the infiltration of leukemic cells is critical for disease progression and relapse. In spite of the canonical functions of histone methylation in gene regulation, differentiation, and DNA homeostasis; its contribution to the nuclear deformability of migrating leukemic cells remains unclear. Here, we showed that 3D conditions promoted a fast upregulation of H3K4 methylation, bound to transcriptional changes in ALL cells. Furthermore, we demonstrated that targeting WDR5 (a core subunit involved in H3K4 methylation) impaired the invasion of leukemia cells in vitro, and their tissue infiltration in an immunodeficient mouse model. WDR5 expression correlated with other cell receptors involved in leukemia dissemination in clinical samples from ALL patients. Interestingly, blocking WDR5 did not reduce the chemotactic response of leukemia cells, suggesting a different mechanism by which H3K4 methylation might operate at both nuclear and functional level to control ALL cell invasiveness in 3D conditions. We applied biochemical and biophysical approaches to determine that H3K4 methylation induced by 3D conditions was dependent on MLCK activity, and regulated the chromatin compaction and the mechanical nuclear response of leukemia cells in 3D conditions. Collectively, our data revealed that confined conditions provide novel molecular and biophysical mechanisms used by leukemia cells to disseminate, suggesting H3K4 methylation and nuclear mechanical pathways as promising therapeutic targets against ALL infiltration.Highlights3D conditions induce H3K4 methylation and transcriptional changes in ALL cells.Targeting WDR5 and H3K4 methylation blocks ALL cell invasion in vitro 3D conditions and leukemia dissemination in vivo.WDR5 expression correlates with other cell receptors related to leukemia migration in clinical samples from patients with ALL.H3K4 methylation induced by 3D conditions is dependent of MLCK activity and regulates cell movement through 3D environments.Leukemia cells in 3D conditions alter their chromatin compaction and the biomechanical deformability of their nuclei.
Generative Adversarial Networks Can Create High Quality Artificial Prostate Cancer Magnetic Resonance Images
Authors: Xu Isaac R. L. , Van Booven Derek J , Goberdhan Sankalp , Breto Adrian L. , Alhusseini Mohammad , Algohary Ahmad , Stoyanova Radka , Punnen Sanoj , Mahne Anton , Arora Himanshu 
Published: June 2022

AbstractPurposeRecent integration of open-source data to machine learning models, especially in the medical field, has opened new doors to study disease progression and/or regression. However, the limitation of using medical data for machine learning approaches is the specificity of data to a particular medical condition. In this context, most recent technologies like generative adversarial networks (GAN) could be used to generate high quality synthetic data that preserves the clinical variability.Materials and MethodsIn this study, we used 139 T2-weighted prostate magnetic resonant images (MRI) from various sources as training data for Single Natural Image GAN (SinGAN), to make a generative model. A deep learning semantic segmentation pipeline trained the model to segment the prostate boundary on 2D MRI slices. Synthetic images with a high-level segmentation boundary of the prostate were filtered and used in the quality control assessment by participating scientists with varying degree of experience (more than 10 years, 1 year, or no experience) to work with MRI images.ResultsThe most experienced participating group correctly identified conventional vs synthetic images with 67% accuracy, the group with 1 year of experience correctly identified the images with 58% accuracy, and group with no prior experience reached 50% accuracy. Nearly half (47%) of the synthetic images were mistakenly evaluated as conventional images. Interestingly, a blinded quality assessment by a board-certified radiologist to differentiate conventional and synthetic images was not significantly different in context of the mean quality of synthetic and conventional images.ConclusionsThis study shows promise that high quality synthetic images from MRI can be generated using GAN. Such an AI model may contribute significantly to various clinical applications which involves supervised machine learning approaches.
Active and passive mechanics for rough terrain traversal in centipedes
Authors: Diaz Kelimar , Erickson Eva , Chong Baxi , Soto Daniel , Goldman Daniel I. 
Published: June 2022

ABSTRACTCentipedes coordinate body and limb flexion to generate propulsion. On flat solid surfaces, the limb-stepping patterns can be characterized according to the direction in which limbaggregates propagate, opposite to (retrograde) or with the direction of motion (direct). It is unknown how limb and body dynamics are modified in terrain with terradynamic complexity more representative of their natural heterogeneous environments. Here, we investigated how centipedes that use retrograde and direct limp-stepping patterns,S. polymorphaandS. sexspinosus, respectively, coordinate their body and limbs to navigate laboratory environments which present footstep challenges and terrain rugosity. We recorded the kinematics and measured the locomotive performance of these animals traversing two rough terrains with randomly distributed step heights and compared the kinematics to those on a flat frictional surface.S. polymorphaexhibited similar body and limb dynamics across all terrains and a decrease in speed with increased terrain roughness. Unexpectedly, when placed in a rough terrain,S. sexspinosuschanged the limb-stepping pattern from direct to retrograde. Further, for both species, traversal of rough terrains was facilitated by hypothesized passive mechanics: upon horizontal collision of a limb with a block, the limb passively bent and later continued the stepping pattern. While centipedes have many degrees of freedom. our results suggest these animals negotiate limb-substrate interactions and navigate complex terrains, by offloading complex control and leveraging the innate flexibility of their limbs.
Factors influencing intentions to use library social media marketing accounts: taking the example of WeChat
Authors: Xin Chen , Yingxi Liu 
Published: June 2022

Purpose
This study aims to explore the factors influencing intentions to use library social media marketing accounts from users’ perspectives to help libraries use social media to provide targeted information services to users to meet their information needs.

Design/methodology/approach
This study is based on the technology acceptance model and theory of planned behaviour and uses WeChat as an example to build the model of factors influencing intentions to use library social media marketing accounts. It takes college students as the research object, performing empirical research through questionnaire surveys and structural equation modeling.

Findings
The results show that attitude, subjective norm and perceived behaviour control have a significant positive impact on library social media marketing – attitude exerts the most significant effect while the impact of perceived usefulness is nonsignificant. Notably, attitude completely mediates perceived usefulness and use intention, while perceived usefulness partially mediates perceived ease of use and attitude. However, birthplace plays a negative moderating role between attitudes and use intention.

Originality/value
This study integrates the theory of planned behaviour and technology acceptance model, discusses the factors influencing intentions to use library social media marketing accounts from the users’ perspectives and proposes strategies and methods for the optimization of library social media marketing. The study helps enhance the effects of library social media marketing by improving the comprehension of current circumstances and influencing factors relevant to this issue.