bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways
Authors: Shrestha Safal , Taujale Rahil , Katiyar Samiksha , Kannan Natarajan 
Published: June 2024

AbstractFructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the Tree of Life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) HepG2 cell line alongside an integrative multi-omics study combining transcriptomics, metabolomics, and interactomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), and carbon and co-factor metabolism. Moreover, enrichment of nicotinamide adenine dinucleotide (NAD) binding proteins and localization of human FN3K (HsFN3K) to mitochondria suggests potential links between FN3K and NAD-mediated energy metabolism and redox balance. We report specific binding of HsFN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. Our studies provide a framework for targeting these understudied kinases in diabetic complications and metabolic disorders where redox balance and NAD-dependent metabolic processes are altered.
Long-term trial of protection provided by adenovirus-vectored vaccine expressing the PPRV H protein
Authors: Darpel Karin E. , Corla Amanda , Stedman Anna , Bellamy Fiona , Flannery John , Rajko-Nenow Paulina , Powers Claire , Wilson Steve , Charleston Bryan , Baron Michael D. , Batten Carrie 
Published: June 2024

AbstractA recombinant, replication-defective, adenovirus-vectored vaccine expressing the H surface glycoprotein of peste des petits ruminants virus (PPRV) has previously been shown to protect goats from challenge with wild-type PPRV at up to 4 months post vaccination. Here, we present the results of a longer-term trial of the protection provided by such a vaccine, challenging animals at 6, 9, 12 and 15 months post vaccination. Vaccinated animals developed high levels of anti-PPRV H protein antibodies, which were virus-neutralising, and the level of these antibodies was maintained for the duration of the trial. The vaccinated animals were largely protected against overt clinical disease from the challenge virus. Although viral genome was intermittently detected in blood samples, nasal and/or ocular swabs of vaccinated goats post challenge, viral RNA levels were significantly lower compared to unvaccinated control animals and vaccinated goats did not appear to excrete live virus. This protection, like the antibody response, was maintained at the same level for at least 15 months after vaccination. In addition, we showed that animals that have been vaccinated with the adenovirus-based vaccine can be revaccinated with the same vaccine after 12 months and showed an increased anti-PPRV antibody response after this boost vaccination. Such vaccines, which provide a DIVA capability, would therefore be suitable for use when the current live attenuated PPRV vaccines are withdrawn at the end of the ongoing global PPR eradication campaign.
De novo design of proteins housing excitonically coupled chlorophyll special pairs
Authors: Ennist Nathan M. , Wang Shunzhi , Kennedy Madison A. , Curti Mariano , Sutherland George A. , Vasilev Cvetelin , Redler Rachel L. , Maffeis Valentin , Shareef Saeed , Sica Anthony V. , Hua Ash Sueh , Deshmukh Arundhati P. , Moyer Adam P. , Hicks Derrick R. , Swartz Avi Z. , Cacho Ralph A. , Novy Nathan , Bera Asim K. , Kang Alex , Sankaran Banumathi , Johnson Matthew P. , Phadkule Amala , Reppert Mike , Ekiert Damian , Bhabha Gira , Stewart Lance , Caram Justin R. , Stoddard Barry L. , Romero Elisabet , Hunter C. Neil , Baker David 
Published: June 2024

AbstractNatural photosystems couple light harvesting to charge separation using a ‘special pair’ of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
Assessing Spatial Representativeness of Global Flux Tower Eddy-Covariance Measurements Using Data from FLUXNET2015
Authors: Fang Junjun , Fang Jingchun , Chen Baozhang , Zhang Huifang , Dilawar Adil , Guo Man , Liu Shu’an 
Published: June 2024

AbstractLarge datasets of carbon dioxide, energy, and water fluxes were measured with the eddy-covariance (EC) technique, such as FLUXNET2015. These datasets are widely used to validate remote-sensing products and benchmark models. One of the major challenges in utilizing EC-flux data is determining the spatial extent to which measurements taken at individual EC towers reflect model-grid or remote sensing pixels. To minimize the potential biases caused by the footprint-to-target area mismatch, it is important to use flux datasets with awareness of the footprint. This study analyze the spatial representativeness of global EC measurements based on the open-source FLUXNET2015 data, using the published flux footprint model (SAFE-f). The calculated annual cumulative footprint climatology (ACFC) was overlaid on land cover and vegetation index maps to create a spatial representativeness dataset of global flux towers. The dataset includes the following components: (1) the ACFC contour (ACFCC) data and areas representing 50%, 60%, 70%, and 80% ACFCC of each site, (2) the proportion of each land cover type weighted by the 80% ACFC (ACFCW), (3) the semivariogram calculated using Normalized Difference Vegetation Index (NDVI) considering the 80% ACFCW, and (4) the sensor location bias (SLB) between the 80% ACFCW and designated areas (e.g. 80% ACFCC and window sizes) proxied by NDVI. Finally, we conducted a comprehensive evaluation of the representativeness of each site from three aspects: (1) the underlying surface cover, (2) the semivariogram, and (3) the SLB between 80% ACFCW and 80% ACFCC, and categorized them into 3 levels. The goal of creating this dataset is to provide data quality guidance for international researchers to effectively utilize the FLUXNET2015 dataset in the future.
A nineteenth-century urban Ottoman population micro dataset: Data extraction and relational database curation from the 1840s pre-census Bursa population registers
Authors: Kabadayı M. Erdem , Erünal Efe 
Published: June 2024

AbstractIn recent decades, the “big microdata revolution” has transformed access to transcribed historical census data for social science research. However, the population records of the Ottoman Empire, spanning Southeastern Europe, Western Asia, and Northern Africa, remained inaccessible to the big microdata ecosystem due to their prolonged unavailability. This publication marks the inaugural release of complete population data for an Ottoman urban center, Bursa, derived from the 1839 population registers. The dataset presents originally non-tabulated register data in a tabular format integrated into a relational Microsoft Access database. Thus, we showcase the extensive and diverse data found in the Ottoman population registers, demonstrating a level of quality and sophistication akin to the censuses conducted worldwide in the nineteenth century. This valuable resource, whose potential has been massively underexploited, is now presented in an accessible format compatible with global microdata repositories. Our aim with this dataset is to enable historical demographic studies for the Ottoman realm and beyond, while also broadening access to the datasets constructed by our large research team.
Power-Doppler-based NH002 microbubble sonoporation with chemotherapy relieves hypoxia and enhances the efficacy of chemotherapy and immunotherapy for pancreatic tumors
Authors: Wu Sheng-Yan , Wang Chung-Hsin , Kang Shih-Tsung , Yu Ching-Fang , Chen Fang-Hsin , Chiang Chi-Shiun 
Published: June 2024

AbstractPancreatic ductal adenocarcinoma (PDAC) poses challenges due to late-stage diagnosis and limited treatment response, often attributed to the hypoxic tumor microenvironment (TME). Sonoporation, combining ultrasound and microbubbles, holds promise for enhancing therapy. However, additional preclinical research utilizing commercially available ultrasound equipment for PDAC treatment while delving into the TME's intricacies is necessary. This study investigated the potential of using a clinically available ultrasound system and phase 2-proven microbubbles to relieve tumor hypoxia and enhance the efficacy of chemotherapy and immunotherapy in a murine PDAC model. This approach enables early PDAC detection and blood-flow-sensitive Power-Doppler sonoporation in combination with chemotherapy. It significantly extended treated mice's median survival compared to chemotherapy alone. Mechanistically, this combination therapy enhanced tumor perfusion and substantially reduced tumor hypoxia (77% and 67%, 1- and 3-days post-treatment). Additionally, cluster of differentiation 8 (CD8) T-cell infiltration increased four-fold afterward. The combined treatment demonstrated a strengthening of the anti-programmed death-ligand 1(αPDL1) therapy against PDAC. Our study illustrates the feasibility of using a clinically available ultrasound system with NH-002 microbubbles for early tumor detection, alleviating hypoxic TME, and improving chemotherapy and immunotherapy. It suggests the development of an adjuvant theragnostic protocol incorporating Power-Doppler sonoporation for pancreatic tumor treatment.
Aloe-inspired eco-friendly synthesis of Ag/ZnO heterostructures: boosting photocatalytic potential
Authors: Ansar Nawal , Shahid Wajeehah , Irshad Muhammad Atif , Shahid Samiah , Nawaz Rab , Irfan Ali , Khan Muhammad Iftikhar , Al-Mutairi Aamal A. , Khizar Maria , Al-Hussain Sami A. , Ullah Sana , Zaki Magdi E. A. 
Published: June 2024

AbstractThe current research focuses on the development of Ag–ZnO heterostructures through a “bottom-up” approach involving the assembly and extraction of Aloe barbadensis Miller gel. These heterostructures composed of metals/semiconductor oxide display distinct and notable optical, electrical, magnetic, and chemical properties that are not found in single constituents and also exhibit photocatalytic applications. These synthesized heterostructures were characterized by XRD, FTIR, SEM, and UV–visible spectroscopy. The high peak intensity of the Ag/ZnO composite shows the high crystallinity. The presence of Ag–O, Zn–O, and O–H bonding is verified using FTIR analysis. SEM analysis indicated the formation of spherical shapes of Ag/ZnO heterostructures. The Zn, O, and Ag elements are further confirmed by EDX analysis. Ag–ZnO heterostructures exhibited excellent photocatalytic activity and stability against the degradation of tubantin red 8BL dye under visible light irradiation.
Climate change impacts on small pelagic fish distribution in Northwest Africa: trends, shifts, and risk for food security
Authors: Sarre Abdoulaye , Demarcq Hervé , Keenlyside Noel , Krakstad Jens-Otto , El Ayoubi Salaheddine , Jeyid Ahmed Mohamed , Faye Saliou , Mbaye Adama , Sidibeh Momodou , Brehmer Patrice 
Published: June 2024

AbstractClimate change is recognised to lead to spatial shifts in the distribution of small pelagic fish, likely by altering their environmental optima. Fish supply along the Northwest African coast is significant at both socio-economic and cultural levels. Evaluating the impacts of climatic change on small pelagic fish is a challenge and of serious concern in the context of shared stock management. Evaluating the impact of climate change on the distribution of small pelagic fish, a trend analysis was conducted using data from 2363 trawl samplings and 170,000 km of acoustics sea surveys. Strong warming is reported across the Southern Canary Current Large Marine Ecosystem (CCLME), extending from Morocco to Senegal. Over 34 years, several trends emerged, with the southern CCLME experiencing increases in both wind speed and upwelling intensity, particularly where the coastal upwelling was already the strongest. Despite upwelling-induced cooling mechanisms, sea surface temperature (SST) increased in most areas, indicating the complex interplay of climatic-related stressors in shaping the marine ecosystem. Concomitant northward shifts in the distribution of small pelagic species were attributed to long-term warming trends in SST and a decrease in marine productivity in the south. The abundance of Sardinella aurita, the most abundant species along the coast, has increased in the subtropics and fallen in the intertropical region. Spatial shifts in biomass were observed for other exploited small pelagic species, similar to those recorded for surface isotherms. An intensification in upwelling intensity within the northern and central regions of the system is documented without a change in marine primary productivity. In contrast, upwelling intensity is stable in the southern region, while there is a decline in primary productivity. These environmental differences affected several small pelagic species across national boundaries. This adds a new threat to these recently overexploited fish stocks, making sustainable management more difficult. Such changes must motivate common regional policy considerations for food security and sovereignty in all West African countries sharing the same stocks.
Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer’s disease-associated metabolites
Authors: Ball Brendan K. , Kuhn Madison K. , Fleeman Bechtel Rebecca M. , Proctor Elizabeth A. , Brubaker Douglas K. 
Published: June 2024

AbstractType 2 diabetes (T2D) is implicated as a risk factor for Alzheimer’s disease (AD), the most common form of dementia. In this work, we investigated neuroinflammatory responses of primary neurons to potentially circulating, blood–brain barrier (BBB) permeable metabolites associated with AD, T2D, or both. We identified nine metabolites associated with protective or detrimental properties of AD and T2D in literature (lauric acid, asparagine, fructose, arachidonic acid, aminoadipic acid, sorbitol, retinol, tryptophan, niacinamide) and stimulated primary mouse neuron cultures with each metabolite before quantifying cytokine secretion via Luminex. We employed unsupervised clustering, inferential statistics, and partial least squares discriminant analysis to identify relationships between cytokine concentration and disease-associations of metabolites. We identified MCP-1, a cytokine associated with monocyte recruitment, as differentially abundant between neurons stimulated by metabolites associated with protective and detrimental properties of AD and T2D. We also identified IL-9, a cytokine that promotes mast cell growth, to be differentially associated with T2D. Indeed, cytokines, such as MCP-1 and IL-9, released from neurons in response to BBB-permeable metabolites associated with T2D may contribute to AD development by downstream effects of neuroinflammation.
Sustained bias of spatial attention in a 3 T MRI scanner
Authors: Smaczny Stefan , Behle Leonie , Kuppe Sara , Karnath Hans-Otto , Lindner Axel 
Published: June 2024

AbstractWhen lying inside a MRI scanner and even in the absence of any motion, the static magnetic field of MRI scanners induces a magneto-hydrodynamic stimulation of subjects’ vestibular organ (MVS). MVS thereby not only causes a horizontal vestibular nystagmus but also induces a horizontal bias in spatial attention. In this study, we aimed to determine the time course of MVS-induced biases in both VOR and spatial attention inside a 3 T MRI-scanner as well as their respective aftereffects after participants left the scanner. Eye movements and overt spatial attention in a visual search task were assessed in healthy volunteers before, during, and after a one-hour MVS period. All participants exhibited a VOR inside the scanner, which declined over time but never vanished completely. Importantly, there was also an MVS-induced horizontal bias in spatial attention and exploration, which persisted throughout the entire hour within the scanner. Upon exiting the scanner, we observed aftereffects in the opposite direction manifested in both the VOR and in spatial attention, which were statistically no longer detectable after 7 min. Sustained MVS effects on spatial attention have important implications for the design and interpretation of fMRI-studies and for the development of therapeutic interventions counteracting spatial neglect.
RoPod, a customizable toolkit for non-invasive root imaging, reveals cell type-specific dynamics of plant autophagy
Authors: Guichard Marjorie , Holla Sanjana , Wernerová Daša , Grossmann Guido , Minina Elena A. 
Published: June 2024

AbstractArabidopsis root is a classic model system in plant cell and molecular biology. The sensitivity of plant roots to local environmental perturbation challenges data reproducibility and incentivizes further optimization of imaging and phenotyping tools. Here we present RoPod, an easy-to-use toolkit for low-stress live time-lapse imaging of Arabidopsis roots. RoPod comprises a dedicated protocol for plant cultivation and a customizable 3D-printed vessel with integrated microscopy-grade glass that serves simultaneously as a growth and imaging chamber. RoPod reduces impact of sample handling, preserves live samples for prolonged imaging sessions, and facilitates application of treatments during image acquisition. We describe a protocol for RoPods fabrication and provide illustrative application pipelines for monitoring root hair growth and autophagic activity. Furthermore, we showcase how the use of RoPods advanced our understanding of plant autophagy, a major catabolic pathway and a key player in plant fitness. Specifically, we obtained fine time resolution for autophagy response to commonly used chemical modulators of the pathway and revealed previously overlooked cell type-specific changes in the autophagy response. These results will aid a deeper understanding of the physiological role of autophagy and provide valuable guidelines for choosing sampling time during end-point assays currently employed in plant autophagy research.
Persistent dysbiosis of duodenal microbiota in patients with controlled pediatric Crohn’s disease after resolution of inflammation
Authors: Pierce Rebecca , Jan Ning-Jiun , Kumar Pankaj , Middleton Jeremy , Petri William A. , Marie Chelsea 
Published: June 2024

AbstractCrohn’s disease is an inflammatory condition of the intestine characterized by largely unknown etiology and a relapse remission cycle of disease control. While possible triggers have been identified, research is inconsistent on the precise cause of these relapses, especially in the under-researched pediatric population. We hypothesized that patients in remission would have persistent microbial and inflammatory changes in small intestinal tissue that might trigger relapse. To this end, we analyzed intestinal biopsy samples from six patients with pediatric Crohn’s disease in remission and a control group of 16 pediatric patients with no evident pathogenic abnormality. We identified compositional microbiota differences, including decreases in the genera Streptococcus and Actinobacillus as well as increases in Oribacterium and Prevotella in patients with controlled Crohn’s disease compared to controls. Further, a histologic analysis found that patients with controlled Crohn’s disease had increased epithelial integrity, and decreased intraepithelial lymphocytes compared with controls. Additionally, we observed increased peripheral CD4+ T cells in patients with pediatric Crohn’s disease. These results indicate that markers of intestinal inflammation are responsive to Crohn’s disease treatment, however the interventions may not resolve the underlying dysbiosis. These findings suggest that persistent dysbiosis may increase vulnerability to relapse of pediatric Crohn’s disease. This study used a nested cohort of patients from the Bangladesh Environmental Enteric Dysfunction (BEED) study (ClinicalTrials.gov ID: NCT02812615 Date of first registration: 24/06/2016).
Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains
Authors: Thakur Niranjan Ravindra , Gorthy Sunita , Vemula AnilKumar , Odeny Damaris A. , Ruperao Pradeep , Sargar Pramod Ramchandra , Mehtre Shivaji Pandurang , Kalpande Hirakant V. , Habyarimana Ephrem 
Published: June 2024

AbstractSorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09–52.55 ppm and 17.92–43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.