bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell quantification of ribosome occupancy in early mouse development
Authors: Ozadam Hakan , Tonn Tori , Han Crystal M. , Segura Alia , Hoskins Ian , Rao Shilpa , Ghatpande Vighnesh , Tran Duc , Catoe David , Salit Marc , Cenik Can 
Published: June 2023

AbstractTranslation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.
Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern
Authors: Shajahan Asif , Pepi Lauren E. , Kumar Bhoj , Murray Nathan B. , Azadi Parastoo 
Published: June 2023

AbstractThe glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N-terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N- and O- glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.
Terfezia boudieri and Terfezia claveryi inhibit the LPS/IFN-γ-mediated inflammation in RAW 264.7 macrophages through an Nrf2-independent mechanism
Authors: Dawood Abdelhameed S. , Sedeek Mohamed S. , Farag Mohamed A. , Abdelnaser Anwar 
Published: June 2023

AbstractDesert truffles have been used as traditional treatments for numerous inflammatory disorders. However, the molecular mechanisms underlying their anti-inflammatory effects in RAW 264.7 macrophages have yet to be fully elucidated. The present study investigated the anti-inflammatory activities of two main desert truffles, Terfezia boudieri and T. claveryi, and the underlying mechanisms associated with their anti-inflammatory activities in RAW 264.7 macrophages stimulated with lipopolysaccharide/interferon-gamma (LPS/IFN-γ). Our results demonstrated that treatment with T. boudieri and T. claveryi extracts effectively suppressed the inflammatory response in LPS/IFN-γ-stimulated RAW 264.7 macrophages. Specifically, T. boudieri extract was found to reduce the production of nitric oxide and inhibit the expression of various pro-inflammatory markers, including inducible nitric oxide synthase, cyclooxygenase-2 (COX-2), tumor necrosis factor-α, and interleukin-6 (IL-6) at both the mRNA and protein levels. Similarly, T. claveryi extract exhibited comparable inhibitory effects, except for the expression of IL-6 and COX-2 at the protein level, where no significant effect was observed. Moreover, both studied extracts significantly downregulated the microRNA expression levels of miR-21, miR-146a, and miR-155, suggesting that T. boudieri and T. claveryi suppress the inflammatory response in LPS/IFN-γ-stimulated RAW 264.7 cells through an epigenetic mechanism. Furthermore, our study reveals a new mechanism for the anti-inflammatory properties of desert truffle extracts. We show for the first time that Terfezia extracts do not rely on the nuclear factor erythroid 2-related factor 2 pathway, previously linked to anti-inflammatory responses. This expands our understanding of natural product anti-inflammatory mechanisms and could have important implications for developing new therapies. To account for differences in truffle effects, extracts prepared were subjected to secondary metabolites profiling using UPLC-MS. UPLC-MS led to the annotation of 87 secondary metabolites belonging to various classes, including amino acids, carbohydrates, alkaloids, amides, fatty acids, sterols, and phenolic compounds. Therefore, these results indicate that T. boudieri and T. claveryi exhibit anti-inflammatory activities through suppressing multiple inflammatory mediators and cytokines and may be potential anti-inflammatory agents.
Scalp acupuncture alleviates cerebral ischemic stroke-induced motor dysfunction in rats via regulating endoplasmic reticulum stress and ER-phagy
Authors: Zhang Yuxin , Lou Huijuan , Lu Jing , Tang Xiaolei , Pang Tingting , Lei Siyuan , Cong Deyu , Wang Yufeng , Sun Liwei 
Published: June 2023

AbstractCerebral ischemic stroke is a high-risk disease and imposes heavy burdens on patients in china. Acupuncture has been used for thousands of years to treat motor dysfunction, cognitive disorder and language barrier caused by cerebral ischemic stroke. Acupoint lines, vertex middle line and anterior oblique line of vertex temple, are always employed to treat cerebral ischemic stroke. However, the mechanism of the two acupoint lines in relieving cerebral ischemic stroke needs further exploration. In the present study, scalp acupuncture treatment alleviated the motor dysfunction, brain damage, and cell death induced by middle cerebral artery occlusion (MCAO) in rats. Proteomics analysis and ultrastructure observation indicated that endoplasmic reticulum and lysosomes might involve in the mechanism of the scalp acupuncture treatment in suppressing MCAO-triggered neural deficits. Effect of the scalp acupuncture treatment on ER stress was then investigated and found that the activation of ER stress mediators, including PERK, IRE1, and ATF6, was downregulated after the scalp acupuncture treatment. Co-localisation analysis of KDEL and CD63 showed that the engulfment of ER fragments by lysosomes was accelerated by the scalp acupuncture treatment. Moreover, expression of pro-apoptotic protein CHOP, phosphorylated-JNK, cleaved capases-3 and -9 also decreased after the scalp acupuncture. In conclusion, the present study showed that scalp acupuncture of vertex middle line and anterior oblique line of vertex temple may alleviate cerebral ischemic stroke by inhibiting ER stress-accelerated apoptosis.
Interoceptive abilities facilitate taking another’s spatial perspective
Authors: Baiano Chiara , Job Xavier , Kirsch Louise P. , Auvray Malika 
Published: June 2023

AbstractInformation can be perceived from a multiplicity of spatial perspectives, which is central to effectively understanding and interacting with our environment and other people. Interoception, the sense of the physiological state of our body, is also a fundamental component contributing to our perception. However, whether the perception of our inner body signals influences our ability to adopt and flexibly change between different spatial perspectives remains poorly understood. To investigate this, 90 participants completed tasks assessing multiple dimensions of interoception (interoceptive sensibility, cardiac interoceptive accuracy and awareness) and the Graphesthesia task to assess tactile spatial perspective-taking and its flexibility. The results revealed that higher cardiac interoceptive awareness is associated with greater consistency in adopting a perspective decentred from the self. Second, higher cardiac interoceptive accuracy was associated with slower and less accurate performance in switching from a decentred to an egocentred perspective. These results show that interoceptive abilities facilitate decentred spatial perspective-taking, likely reflecting stronger perceived boundaries between internal states and the external world.
Risk of developing chronic kidney disease in young-onset Type 2 diabetes in Korea
Authors: Lee Joonyub , Lee Seung-Hwan , Yoon Kun-Ho , Cho Jae Hyoung , Han Kyungdo , Yang Yeoree 
Published: June 2023

AbstractWe investigated the risk of developing chronic kidney disease (CKD) in patients with young-onset Type 2 diabetes (YOD, diagnosed age < 40 years). We enrolled 84,384 patients aged 20–64 who started anti-diabetic medication between 2010 and 2011 from the Korea National Health Insurance Sharing Service; patients with Type 1 diabetes or a history of CKD were excluded. Multivariate logistic regression analyses were performed to adjust for YOD-distinct variables and compare the incidence of CKD between YOD and late-onset diabetes (LOD, diagnosed age ≥ 40 years). During the median observation period of 5.16 years (interquartile range: 4.58–5.77 years), 1480 out of 77,039 LOD patients and 34 out of 7345 YOD patients developed CKD. Patients with YOD had distinct baseline characteristics compared with the patients with LOD. The odds ratio of developing CKD in patients with YOD over LOD was 1.70 (95% CI 1.15–2.51) after adjusting clinically distinct variables. The increased CKD odds in YOD compared with LOD was greater in the non-smoking group (OR 2.03, 95% CI 1.26–3.26) than in the smoking group (OR 1.49, 95% CI 0.74–2.98, p = 0.0393 for interaction). Among YOD patients, hypertension (34.76% vs. 64.71%, p = 0.0003), dyslipidemia (46.87% vs. 73.53%, p = 0.0019), and sulfonylurea use (35.54% vs. 52.94%, p = 0.0345) were associated with CKD development. YOD patients have a greater risk of developing CKD than LOD patients after adjusting clinically distinct variables.
FRET analysis of the temperature-induced structural changes in human TRPV3
Authors: Kim Jinyoung , Won Jongdae , Chung Dong Kyu , Lee Hyung Ho 
Published: June 2023

AbstractTransient receptor potential vanilloid member 3 (TRPV3) is an ion channel that plays a critical role in temperature sensing in skin. There have been active studies on how TRPV3, which is also known as one of the temperature-sensitive transient receptor potential (thermoTRP) channels, responds to temperature. However, the previous studies were mostly based on TRPV3 originating from mice or rats. Here, we focus on human TRPV3 (hTRPV3) and show that which domain of hTRPV3 undergoes conformational changes as temperature increases by Förster resonance energy transfer (FRET) assay. During the heat-induced activation of hTRPV3, the linker domain close to C-terminus, that is, the C-terminal domain shows a largest structural change whereas there is little change in the ankyrin repeat domain (ARD). Interestingly, the activation of hTRPV3 by an agonist shows structural change patterns that are completely different from those observed during activation by heat; we observe structural changes in ARD and S2–S3 linker after ligand stimulation whereas relatively little change is observed when stimulated by heat. Our results provide insight into the thermal activation of hTRPV3 channel.
A causal link between mental imagery and affect-laden perception of climate change related risks
Authors: Karlsson Hulda , Asutay Erkin , Västfjäll Daniel 
Published: June 2023

AbstractPrevious studies have shed light on the importance of affect in risk perception and the role of mental imagery in generating affect. In the current study, we explore the causal relationship between mental imagery, affect, and risk perception by systematically varying the level of mental imagery in three levels (i.e., enhanced, spontaneous, or prevented). In light of the increasing environmental risk of adverse events caused by climate change, we operationalize risk as participants' perceived risk of climate change. One-thousand-fifty-five participants were recruited online and randomized to one of three levels of mental imagery. As predicted, we found a causal link between the level of mental imagery, affective experience, and perceived risk of climate change, in that enhanced mental imagery caused a larger decrease in positive affective valence and a larger increase in perceived risk of climate change. We argue that mental imagery enhances the negative affect associated with the risk event by creating a perceptual experience that mimics seeing the environmental risk events.
Changes in pre- and in-hospital management and outcomes among children with out-of-hospital cardiac arrest between 2012 and 2017 in Kanto, Japan
Authors: Ishihara Tadashi , Sasaki Ryuji , Enomoto Yuki , Amagasa Shunsuke , Yasuda Masato , Ohnishi Shima 
Published: June 2023

AbstractPreviously, the SOS-KANTO 2012 studies, conducted in the Kanto area of Japan, reported a summary of outcomes in patients with out-of-hospital cardiac arrest (OHCA). This sub-analysis of the SOS-KANTO study 2017 aimed to evaluate the neurological outcomes of paediatric OHCA patients, by comparing the SOS-KANTO 2012 and 2017 studies. All OHCA patients, aged < 18 years, who were transported to the participating hospitals by EMS personnel were included in both SOS-KANTO studies (2012 and 2017). The number of survival patients with favourable neurological outcomes (paediatric cerebral performance category 1 or 2) at 1 month did not improve between 2012 and 2017. There was no significant difference in achievement of pre-hospital return of spontaneous circulation (ROSC) [odds ratio (OR): 2.00, 95% confidence interval (95% CI): 0.50–7.99, p = 0.50] and favourable outcome at 1 month [OR: 0.67, 95% CI: 0.11–3.99, p = 1] between the two studies, matched by age, witnessed arrest, bystander CPR, aetiology of OHCA, and time from call to EMS arrival. Multivariable logistic regression showed no significant difference in the achievement of pre-hospital ROSC and favourable outcomes at 1 month between the two studies.
Thermal aerial culling for the control of vertebrate pest populations
Authors: Cox Tarnya E. , Paine David , O’Dwyer-Hall Emma , Matthews Robert , Blumson Tony , Florance Brenton , Fielder Kate , Tarran Myall , Korcz Matt , Wiebkin Annelise , Hamnett Peter W. , Bradshaw Corey J. A. , Page Brad 
Published: June 2023

AbstractHelicopter-based shooting is an effective management tool for large vertebrate pest animals. However, animals in low-density populations and/or dense habitat can be difficult to locate visually. Thermal-imaging technology can increase detections in these conditions. We used thermal-imaging equipment with a specific helicopter crew configuration to assist in aerial culling for feral pigs (Sus scrofa) and fallow deer (Dama dama) in South Australia in 2021. Seventy-two percent of pigs and 53% of deer were first detected in dense canopy/tall forest habitat. Median time from the first impact shot to incapacitation was < 12 s. The culling rate (animals hour−1) doubled compared to visual shoots over the same populations and the wounding rate was zero resulting in a incapacitation efficiency of 100%. The crew configuration gave the shooter a wide field of view and the thermal operator behind the shooter provided essential support to find new and escaping animals, and to confirm species identification and successful removal. The crew configuration allowed for successful target acquisition and tracking, with reduced target escape. The approach can increase the efficiency of aerial culling, has the potential to increase the success of programs where eradication is a viable option, and can improve animal welfare outcomes by reducing wounding rates and the escape of target animals.
Transcriptome changes during osteogenesis of porcine mesenchymal stem cells derived from different types of synovial membranes and genetic background
Authors: Li Shuaichen , Siengdee Puntita , Oster Michael , Reyer Henry , Wimmers Klaus , Ponsuksili Siriluck 
Published: June 2023

AbstractSynovial membrane mesenchymal stem cells (SMSCs) often serve as in vitro model for bone disease, but the molecular mechanisms driving osteogenesis in SMSCs from different donor cells of various sources and breeds remain unclear. In this study, porcine SMSCs isolated from adipose synovium (FP) and fibrous synovium (FS) of Angeln Saddleback (AS) and German Landrace (DL) were used to discover the signaling network change after osteogenic induction. During osteogenic differentiation, mineral deposition was first observed at day 14 and further increased until day 21. Transcriptional changes between day 1 and day 21 were enriched in several signaling pathways, including Wnt, PI3K-Akt, and TGF-beta pathway. Certain pathways related to osteogenesis, including osteoblast differentiation, regulation of bone mineralization, and BMP signaling pathway, were enriched at late time points, as confirmed by the osteogenic markers ALPL, COL1A1, and NANOG. A fraction of differentially expressed genes (DEGs) were found between FP and FS, while DEGs between AS and DL increased during the differentiation phase until day 7 and then decreased from day 14 to day 21. These genes are involved in several important signaling pathways, including TGF-beta, Wnt, and lipid-related signaling pathways, suggesting that SMSCs from these two breeds have different osteogenic capabilities.
Usefulness of two-dimensional shear wave elastography in the assessment of non-alcoholic fatty liver disease in children and adolescents
Authors: Yoon Jong Seo , Lim Kyoung Ja , Hwang Il Tae 
Published: June 2023

AbstractTwo-dimensional shear wave elastography (2D-SWE) evaluates liver stiffness using a non-invasive method, but studies in the paediatric population are rare. This study evaluated the role of 2D-SWE in the diagnosis and severity of paediatric non-alcoholic fatty liver disease (NAFLD). In total, 131 patients with NAFLD and 25 healthy controls were enrolled in this study. The diagnosis and severity of NAFLD were initially assessed using the ultrasound fatty liver index (US-FLI), and all participants underwent 2D-SWE. US-FLI semi-quantitatively measures the severity of NAFLD on a scale of 2–8. The assessment of liver stiffness measurement (LSM) by 2D-SWE is presented in kilopascals (kPa). The NAFLD group was characterised by significantly higher LSM (4.40 ± 0.90 kPa) than the control group (3.76 ± 0.28 kPa) (P < 0.001). 2D-SWE significantly correlated with age, height, weight, body mass index, glucose, aspartate aminotransferase, alanine aminotransferase, high-density lipoprotein cholesterol, US-FLI, and triglyceride-glucose index (P < 0.001). In the receiver operating characteristic curve analysis, the area under the curve of LSM for predicting US-FLI ≥ 2 and ≥ 6 was 0.784 (P < 0.001) and 0.819 (P < 0.001), respectively. In conclusion, we suggest that 2D-SWE can be used as a non-invasive diagnostic tool for diagnosing and assessing the severity of paediatric NAFLD.
Biomolecular condensates – extant relics or evolving microcompartments?
Authors: Rangachari Vijayaraghavan 
Published: June 2023

AbstractUnprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.
Unsupervised deep homography with multi‐scale global attention
Authors: Hu Wei , He Chu , Lin Mingyuan , Zhou Haoyu 
Published: June 2023

AbstractHomography estimation serves an important role in many computer vision tasks. Depending heavily on hand‐craft feature quality, traditional methods degenerate sharply in scenes with low texture. Existing deep homography methods can handle the low‐texture problem but are not robust for scenes with low overlap rates and/or illumination changes. This paper proposes a novel unsupervised homography estimation method that can simultaneously handle such low overlap and illumination change. Specifically, a powerful module, named global transformer contextual encoder (GTCE) is first designed, together with a correlation encoder to effectively aggregate global contextual information and reduce matching ambiguity between feature maps. Moreover, a hybrid photo‐perceptual loss for unsupervised homography estimation is proposed. The proposed loss function considers alignment information on both pixel level and perceptual level thus helping this network to be more adaptive to various scenes, including normal cases and illumination change cases. The results of extensive experiments on synthetic and real‐world datasets demonstrate the superiority of this proposed method over current state‐of‐the‐art solutions especially on challenging scenes with low overlap rates, repetitive patterns and illumination changes.