bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lightning‐Produced Nitrogen Oxides Per Flash Length Obtained by Using TROPOMI Observations and the Ebro Lightning Mapping Array
Authors: Pérez‐Invernón Francisco J. , Gordillo‐Vázquez Francisco J. , van der Velde Oscar , Montanyá Joan , López Trujillo Jesús Alberto , Pineda Nicolau , Huntrieser Heidi , Valks Pieter , Loyola Diego , Seo Sora , Erbertseder Thilo 
Published: December 2023

AbstractLightning is one of the main sources of NOx in the Earth's atmosphere. However, there is a large variability in NOx production during the lifetime of thunderstorms. In this study, we used the TROPOspheric Monitoring Instrument (TROPOMI) cloud and NO2 research products along with Lightning Mapping Array (LMA) measurements to investigate the possible relation between the amount of NOx produced per lightning flash and flash channel length in the Ebro Valley. We found that there is a positive relationship between both variables. In turn, the vertical structure of the analyzed lightning flashes indicates that longer flashes could release more LNOx at lower altitudes than shorter flashes, while higher flash rates produce less LNOx per flash.
Examining the Water Scarcity Vulnerability in US River Basins Due To Changing Climate
Authors: Wolkeba Fitsume T. , Kumar Mukesh , Mekonnen Mesfin M. 
Published: December 2023

AbstractAccurate assessment of changes in water availability with changing climate is vital for effective mitigation and adaptation. In this research, we employ a parsimonious Budyko curve method to evaluate changes in water availability under low‐ (SSP126) and high‐emission (SSP585) scenarios for 331 river basins in the contiguous United States. We also assess the relative role of changes in precipitation (∆P) and potential evapotranspiration (∆PET) with changing climate on the increase in water availability vulnerability. Results highlight that around 43% (28%) of basins are projected to experience increased vulnerability to changing climate in high‐emission (low‐emission) scenarios. Sub‐humid basins are most often impacted, while arid and semi‐arid basins exhibit lower sensitivity to changes. Intriguingly, ∆PET emerges as the dominant control on vulnerability, surpassing ∆P, particularly under SSP585 scenario. The analysis prompts water managers to focus on long‐term mitigation planning and scientists to further constraint climate and water budget forecasts in affected basins.
Trace Metal Fluxes of Cd, Cu, Pb and Zn From the Congo River Into the South Atlantic Ocean Are Supplemented by Atmospheric Inputs
Authors: Liu Te , Hopwood Mark J. , Krisch Stephan , Vieira Lúcia H. , Achterberg Eric P. 
Published: December 2023

AbstractThe Congo River supplies vast quantities of trace metals (TMs) to the South Atlantic Ocean, but TM budgets for the Congo plume derived using radium isotopes for GEOTRACES cruise GA08 suggest additional input other than the river outflow. Considering the tight correlations between most dissolved TMs and salinity in the plume and the high rainfall during the wet season over the Congo shelf, we hypothesized that wet atmospheric deposition is a TM source to the Congo plume. Observed TM concentrations in rainwaters across the Congo shelf were mostly comparable to values from previous work in the North Atlantic and Mediterranean Sea. Wet deposition contributed the equivalent of 43% dCd, 21% dCu, 20% dPb and 68% dZn of the Congo River fluxes. Our findings show an important role of wet deposition in supplying TMs to the South Atlantic overlapping with the region that receives substantial TM fluxes from the Congo River.
Therapeutic cancer vaccines: advancements, challenges and prospects
Authors: Fan Ting , Zhang Mingna , Yang Jingxian , Zhu Zhounan , Cao Wanlu , Dong Chunyan 
Published: December 2023

AbstractWith the development and regulatory approval of immune checkpoint inhibitors and adoptive cell therapies, cancer immunotherapy has undergone a profound transformation over the past decades. Recently, therapeutic cancer vaccines have shown promise by eliciting de novo T cell responses targeting tumor antigens, including tumor-associated antigens and tumor-specific antigens. The objective was to amplify and diversify the intrinsic repertoire of tumor-specific T cells. However, the complete realization of these capabilities remains an ongoing pursuit. Therefore, we provide an overview of the current landscape of cancer vaccines in this review. The range of antigen selection, antigen delivery systems development the strategic nuances underlying effective antigen presentation have pioneered cancer vaccine design. Furthermore, this review addresses the current status of clinical trials and discusses their strategies, focusing on tumor-specific immunogenicity and anti-tumor efficacy assessment. However, current clinical attempts toward developing cancer vaccines have not yielded breakthrough clinical outcomes due to significant challenges, including tumor immune microenvironment suppression, optimal candidate identification, immune response evaluation, and vaccine manufacturing acceleration. Therefore, the field is poised to overcome hurdles and improve patient outcomes in the future by acknowledging these clinical complexities and persistently striving to surmount inherent constraints.
Elevated peripheral levels of receptor-interacting protein kinase 1 (RIPK1) and IL-8 as biomarkers of human amyotrophic lateral sclerosis
Authors: Wei Jun , Li Min , Ye Zhi , Hu Xinqian , He Xiaoyan , Wang Jia , Chen Gaofeng , Zou Chengyu , Xu Daichao , Zhang Hongbing , Yuan Junying , Zha Yunhong 
Published: December 2023

AbstractAmyotrophic lateral sclerosis (ALS) is a devastating fatal neurodegenerative disease with no cure. Receptor-interacting protein kinase 1 (RIPK1) has been proposed to mediate pathogenesis of ALS. Primidone has been identified as an old drug that can also inhibit RIPK1 kinase. We conducted a drug-repurposing biomarker study of primidone as a RIPK1 inhibitor using SOD1G93A mice and ALS patients. SOD1G93A mice treated with primidone showed significant delay of symptomatic onset and improved motor performance. One-hundred-sixty-two ALS participants dosed daily with primidone (62.5 mg) completed 24-week follow-up. A significant reduction was showed in serum levels of RIPK1 and IL-8, which were significantly higher in ALS patients than that of healthy controls (P < 0.0001). Serum RIPK1 levels were correlated positively with the severity of bulbar symptoms (P < 0.05). Our study suggests that serum levels of RIPK1 and IL-8 in peripheral can be used as clinical biomarkers for the activation of RIPK1 in central nervous system in human ALS patients. Repurposing primidone may provide a promising therapeutic strategy for ALS. The effect of primidone for the treatment of other inflammatory diseases may also be considered, since the activation of RIPK1 has been implicated in mediating a variety of inflammatory diseases including COVID-19-associated cytokine release syndrome (CRS). (ChiCTR2200060149).
DPPIV+ fibro-adipogenic progenitors form the niche of adult skeletal muscle self-renewing resident macrophages
Authors: Babaeijandaghi Farshad , Kajabadi Nasim , Long Reece , Tung Lin Wei , Cheung Chun Wai , Ritso Morten , Chang Chih-Kai , Cheng Ryan , Huang Tiffany , Groppa Elena , Jiang Jean X. , Rossi Fabio M. V. 
Published: December 2023

AbstractAdult tissue-resident macrophages (RMs) are either maintained by blood monocytes or through self-renewal. While the presence of a nurturing niche is likely crucial to support the survival and function of self-renewing RMs, evidence regarding its nature is limited. Here, we identify fibro-adipogenic progenitors (FAPs) as the main source of colony-stimulating factor 1 (CSF1) in resting skeletal muscle. Using parabiosis in combination with FAP-deficient transgenic mice (PdgfrαCreERT2× DTA) or mice lacking FAP-derived CSF1 (PdgfrαCreERT2× Csf1flox/null), we show that local CSF1 from FAPs is required for the survival of both TIM4- monocyte-derived and TIM4+ self-renewing RMs in adult skeletal muscle. The spatial distribution and number of TIM4+ RMs coincide with those of dipeptidyl peptidase IV (DPPIV)+ FAPs, suggesting their role as CSF1-producing niche cells for self-renewing RMs. This finding identifies opportunities to precisely manipulate the function of self-renewing RMs in situ to further unravel their role in health and disease.
Atypical flagella assembly and haploid genome coiling during male gamete formation in Plasmodium
Authors: Hair Molly , Moreira-Leite Flávia , Ferguson David J. P. , Zeeshan Mohammad , Tewari Rita , Vaughan Sue 
Published: December 2023

AbstractGametogenesis in Plasmodium spp. occurs within the Anopheles mosquito and is essential for sexual reproduction / differentiation and onwards transmission to mammalian hosts. To better understand the 3D organisation of male gametogenesis, we used serial block face scanning electron microscopy (SBF-SEM) and serial-section cellular electron tomography (ssET) of P. berghei microgametocytes to examine key structures during male gamete formation. Our data reveals an elaborate organisation of axonemes coiling around the nucleus in opposite directions forming a central axonemal band in microgametocytes. Furthermore, we discover the nucleus of microgametes to be tightly coiled around the axoneme in a complex structure whose formation starts before microgamete emergence during exflagellation. Our discoveries of the detailed 3D organisation of the flagellated microgamete and the haploid genome highlight some of the atypical mechanisms of axoneme assembly and haploid genome organisation during male gamete formation in the malaria parasite.
Accessing gold p-acid reactivity under electrochemical anode oxidation (EAO) through oxidation relay
Authors: Zhang Shuyao , Wei Jingwen , Ye Xiaohan , Perez Angel , Shi Xiaodong 
Published: December 2023

AbstractThe gold π-acid activation under electrochemical conditions is achieved. While EAO allows easy access to gold(III) intermediates over alternative chemical oxidation under mild conditions, the reported examples so far are limited to coupling reactions due to the rapid AuIII reductive elimination. Using aryl hydrazine-HOTf salt as precursors, the π-activation reaction mode was realized through oxidation relay. Both alkene and alkyne di-functionalization were achieved with excellent functional group compatibility and regioselectivity, which extended the versatility and utility of electrochemical gold redox chemistry for future applications.
Selenium-based metabolic oligosaccharide engineering strategy for quantitative glycan detection
Authors: Tian Xiao , Zheng Lingna , Wang Changjiang , Han Yida , Li Yujie , Cui Tongxiao , Liu Jialin , Liu Chuanming , Jia Guogeng , Yang Lujie , Hsu Yi , Zeng Chen , Ding Lijun , Wang Chu , Cheng Bo , Wang Meng , Xie Ran 
Published: December 2023

AbstractMetabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and the background signal readout makes it challenging to achieve glycan quantification. Here we develop SeMOE, a selenium-based metabolic oligosaccharide engineering strategy that concisely combines elemental analysis and MOE,enabling the mass spectrometric imaging of glycome. We also demonstrate that the new-to-nature SeMOE probes allow for detection, quantitative measurement and visualization of glycans in diverse biological contexts. We also show that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. SeMOE thus provides a convenient and simplified method to explore the glyco-world.
Molecular mechanism of phospholipid transport at the bacterial outer membrane interface
Authors: Yeow Jiang , Luo Min , Chng Shu-Sin 
Published: December 2023

AbstractThe outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
A rule-free workflow for the automated generation of databases from scientific literature
Authors: Gilligan Luke P. J. , Cobelli Matteo , Taufour Valentin , Sanvito Stefano 
Published: December 2023

AbstractIn recent times, transformer networks have achieved state-of-the-art performance in a wide range of natural language processing tasks. Here we present a workflow based on the fine-tuning of BERT models for different downstream tasks, which results in the automated extraction of structured information from unstructured natural language in scientific literature. Contrary to existing methods for the automated extraction of structured compound-property relations from similar sources, our workflow does not rely on the definition of intricate grammar rules. Hence, it can be adapted to a new task without requiring extensive implementation efforts and knowledge. We test our data-extraction workflow by automatically generating a database for Curie temperatures and one for band gaps. These are then compared with manually curated datasets and with those obtained with a state-of-the-art rule-based method. Furthermore, in order to showcase the practical utility of the automatically extracted data in a material-design workflow, we employ them to construct machine-learning models to predict Curie temperatures and band gaps. In general, we find that, although more noisy, automatically extracted datasets can grow fast in volume and that such volume partially compensates for the inaccuracy in downstream tasks.
MELD-Na score may underestimate disease severity and risk of death in patients with metabolic dysfunction-associated steatotic liver disease (MASLD)
Authors: Yardeni David , Shiloh Adi , Lipnizkiy Inna , Nevo-Shor Anat , Abufreha Naim , Munteanu Daniela , Novack Victor , Etzion Ohad 
Published: December 2023

AbstractPortal hypertension often precedes the development of advanced fibrosis in patients with Metabolic dysfunction-associated steatotic liver disease (MASLD) and may accelerate disease progression to cirrhosis. We aimed to evaluate whether prioritization tools accurately predict survival in patients with MASLD and clinically significant portal hypertension (CSPH). We retrospectively identified patients diagnosed with esophageal or gastric varices (EGV). Laboratory results, endoscopy reports and outcomes of patients with MASLD were compared to patients with advanced stage chronic liver disease (CLD) of other etiologies. During the study period 326 patients were diagnosed with EGV. 88 (26.9%) had MASLD, 113 (34.6%) viral hepatitis (VH), 63 (19.3%) alcoholic liver disease (ALD) and 62 (19%) both VH and ALD (VHALD). EGV bleeding events were significantly more frequent in patients with MASLD (36.3%), compared to VH (28.3%), ALD (30.1%) and VHALD (25.8%), respectively (p < 0.01). Mean Model for End-Stage Liver Disease (MELD)-Na score surrounding 1 year of first event of EGV bleeding was significantly lower in MASLD patients compared to all other etiologies (p = 0.02). At a MELD-Na score of 11–20, cumulative survival rate was significantly lower in MASLD patients compared to all other etiologies (log rank p < 0.01). MASLD patients present with EGV bleeding at lower MELD-Na scores compared to other etiologies of CLD. MELD-Na score may therefore underestimate disease severity and risk of death in patients with MASLD and CSPH.
Examining the rural–urban differentials in yoga and mindfulness practices among middle-aged and older adults in India: secondary analysis of a national representative survey
Authors: Sahoo Umakanta , Sharma Santosh K. , Chari Harshita , Nayak Soumya Ranjan , Ali Waad , Muhammad T. 
Published: December 2023

AbstractPhysical activity and mental well-being play an important role in reducing the risk of various diseases and in promoting independence among older adults. Appropriate physical activity, including yoga and mindfulness practices, can help rectify the loss of independence due to aging and have a positive influence on physical health and functional activities. This study assessed rural–urban differences in yoga and mindfulness practices and their associated factors among middle-aged and older Indian adults. The total sample size considered for the current analysis was 72,250 middle-aged and older adults (aged ≥ 45 years). Bivariate and multivariable logistic regression analyses were used to estimate the prevalence of yoga and mindfulness practices and examine the associations of selected variables with yoga and mindfulness practices among the participants. Further, we used the Fairley decomposition technique to determine the factors contributing to rural–urban differences in the prevalence of yoga and mindfulness practices among middle-aged and older adults. More than 9% of middle-aged and older adults in rural areas and 14% in urban areas reported practicing yoga and mindfulness activities more than once per week. Adults aged ≥ 65 years were more likely to practice yoga and mindfulness activities than those who age 45–54 years were. Those with an education of ten years and above were 2.3 and 2.1 times higher likely to practice yoga in rural (AOR: 2.28; CI: 2.07–2.52) and urban (AOR: 2.13; CI: 1.91–2.37) areas compared to their uneducated peers, respectively. The largest contributors in diminishing the gap in yoga practice among participants were education (44.2%), caste (2.5%), chronic diseases such as hypertension (4.53%), diabetes (1.71%), high cholesterol (3.08%), self-reported pain (5.76%), and difficulties in instrumental activities of daily living (1.22%). The findings suggest that middle-aged and older adults in urban areas practice yoga and mindfulness activities more than their peers in rural areas do. Education level, household characteristics, and health outcomes such as chronic conditions, pain, and functional difficulties explain the observed differences in yoga and mindfulness practices across rural and urban areas. Age-appropriate healthy practices such as yoga and mindfulness should be encouraged to enhance the physical and mental well-being of middle-aged and older adults, especially in rural areas.
Evaluation of antibacterial properties of nisin peptide expressed in carrots
Authors: Fallah Ziarani Masoumeh , Tohidfar Masoud , Mirjalili Mohammad Hossein 
Published: December 2023

AbstractNisin, derived from Lactococcus lactis, is a well-known natural food preservative. In the present study, the gene of nisin was transformed to carrot by Agrobacterium tumefaciens strain LBA4404 harboring the recombinant binary vector pBI121 containing neomycin phosphotransferase II (nptII) gene, peptide signal KDEL, and Kozak sequence. The integration of nisin and nptII transgenes into the plant genome was confirmed by polymerase chain reaction (PCR) and dot blot analysis. The gene expression was also performed by RT-PCR and Enzyme-Linked Immunosorbent Assay. The level of nisin expressed in one gram of transgenic plant ranged from 0.05 to 0.08 μg/ml. The stability of nisin varied in orange and peach juices depending on the temperature on the 70th day. The leaf protein extracted from the transgenic plant showed a significant preservative effect of nisin in peach and orange juice. A complete inhibition activity against Staphylococcus aureus and Escherichia coli in orange juice was observed within 24 h. After 24 h, log 1 and log 2 were obtained in a peach juice containing Staphylococcus aureus and Escherichia coli, respectively. Results of HPLC indicated that Chlorogenic and Chicoric acid compounds were increased in transgenic plants, but this increase was not significant. The study of determining the genetic stability of transgenic plants in comparison with non-transgenic plants showed high genetic stability between non-transgenic plants and transgenic plants. This study confirmed the significant inhibitory effect of nisin protein on gram-positive and gram-negative bacteria.
Potential biodegradation of polycyclic aromatic hydrocarbons (PAHs) and petroleum hydrocarbons by indigenous fungi recovered from crude oil-contaminated soil in Iran
Authors: Fallahi Maryam , Sarempour Mohammadsaeed , Mirzadi Gohari Amir 
Published: December 2023

AbstractA total of 265 fungal individuals were isolated from soils exposed to heavy oil spills in the Yadavaran oil field in Iran to discover indigenous fungal species with a high potential to biodegrade petroleum hydrocarbon pollutants. Morphological and molecular identification of obtained fungal species led to their assignment into 16 genera and 25 species. Alternaria spp. (78%), Fusarium spp. (5%), and Cladosporium spp. (4%) were the most common genera, along with Penicillium spp., Neocamarosporium spp., Epicoccum sp., Kotlabaea sp., Aspergillus sp., Mortierella sp., and Pleurotus sp. A preliminary screening using the DCPIP indicator revealed that approximately 35% of isolates from Alternaria, Epicoccum, Neocamarosporium, Cladosporium, Fusarium, Stachybotrys, Penicillium, and Stemphylium demonstrated promising tolerance to crude oil. The best-performing isolates (12 fungal individuals) were further investigated for their capacity to mineralize a mixture of four polycyclic aromatic hydrocarbons (PAH) for 47 days, quantified by GC–MS. Eventually, two top-performing isolates, namely 5c-12 (Alternaria tenuissima) and 3b-1 (Epicoccum nigrum), were applied to petroleum-contaminated soil. The GC–MS analysis showed that 60 days after inoculation, these isolates successfully degraded more than 70% of the long-chain hydrocarbons in the soil, including C8-C16 n-alkanes, C36 n-alkane, and Pristane. This study introduces two fungal species (5c-12 and 3b-1) with high potential for biodegrading petroleum compounds and PAHs, offering promising prospects for the decontamination of oil-contaminated soil.