bluuebunny/crossref_metadata_2025_split huggingface dataset:
The HIV-1 capsid core is an opportunistic nuclear import receptor
Authors: Xue Guangai , Yu Hyun Jae , Buffone Cindy , Huang Szu-Wei , Lee KyeongEun , Goh Shih Lin , Gres Anna T. , Guney Mehmet Hakan , Sarafianos Stefan G. , Luban Jeremy , Diaz-Griffero Felipe , KewalRamani Vineet N. 
Published: June 2023

AbstractThe movement of viruses and other large macromolecular cargo through nuclear pore complexes (NPCs) is poorly understood. The human immunodeficiency virus type 1 (HIV-1) provides an attractive model to interrogate this process. HIV-1 capsid (CA), the chief structural component of the viral core, is a critical determinant in nuclear transport of the virus. HIV-1 interactions with NPCs are dependent on CA, which makes direct contact with nucleoporins (Nups). Here we identify Nup35, Nup153, and POM121 to coordinately support HIV-1 nuclear entry. For Nup35 and POM121, this dependence was dependent cyclophilin A (CypA) interaction with CA. Mutation of CA or removal of soluble host factors changed the interaction with the NPC. Nup35 and POM121 make direct interactions with HIV-1 CA via regions containing phenylalanine glycine motifs (FG-motifs). Collectively, these findings provide additional evidence that the HIV-1 CA core functions as a macromolecular nuclear transport receptor (NTR) that exploits soluble host factors to modulate NPC requirements during nuclear invasion.
Formation mechanism of high-index faceted Pt-Bi alloy nanoparticles by evaporation-induced growth from metal salts
Authors: Koo Kunmo , Shen Bo , Baik Sung-Il , Mao Zugang , Smeets Paul J. M. , Cheuk Ivan , He Kun , dos Reis Roberto , Huang Liliang , Ye Zihao , Hu Xiaobing , Mirkin Chad A. , Dravid Vinayak P. 
Published: June 2023

AbstractNanoparticles with high-index facets are intriguing because such facets can lend the structure useful functionality, including enhanced catalytic performance and wide-ranging optical tunability. Ligand-free solid-state syntheses of high index-facet nanoparticles, through an alloying-dealloying process with foreign volatile metals, are attractive owing to their materials generality and high yields. However, the role of foreign atoms in stabilizing the high-index facets and the dynamic nature of the transformation including the coarsening and facet regulation process are still poorly understood. Herein, the transformation of Pt salts to spherical seeds and then to tetrahexahedra, is studied in situ via gas-cell transmission electron microscopy. The dynamic behaviors of the alloying and dealloying process, which involves the coarsening of nanoparticles and consequent facet regulation stage are captured in the real time with a nanoscale spatial resolution. Based on additional direct evidence obtained using atom probe tomography and density functional theory calculations, the underlying mechanisms of the alloying-dealloying process are uncovered, which will facilitate broader explorations of high-index facet nanoparticle synthesis.
Scientific perspectives on lunar exploration in Europe
Authors: Flahaut Jessica , van der Bogert Carolyn H. , Crawford Ian A. , Vincent-Bonnieu Sebastien 
Published: June 2023

AbstractThe Moon is a geological history book, preserving information about the history of the Solar System, including the formation and early evolution of the terrestrial planets and their bombardment histories, as well as providing insight into other fundamental Solar System processes. These topics form the basis for science “of the Moon”, but the lunar surface is also a platform for science “on the Moon” and “from the Moon”—including astronomical observations, fundamental physics, and life science investigations. Recently, the Moon has become a destination for technology research and development—in particular for developing in situ resources, human exploration, and habitation, and for its potential use as a waypoint for the human exploration of Mars. This paper, based on recommendations originally proposed in a White Paper for ESA’s SciSpacE strategy, outlines key lunar science questions that may be addressed by future space exploration missions and makes recommendations for the next decades.
A guide to sharing open healthcare data under the General Data Protection Regulation
Authors: de Kok Jip W. T. M. , de la Hoz Miguel Á. Armengol , de Jong Ymke , Brokke Véronique , Elbers Paul W. G. , Thoral Patrick , Castillejo Alejandro , Trenor Tomás , Castellano Jose M. , Bronchalo Alberto E. , Merz Tobias M. , Faltys Martin ,   Collaborator group, Casares Cristina , Jiménez Araceli , Requejo Jaime , Gutiérrez Sonia , Curto David , Rätsch Gunnar , Peppink Jan M. , Driessen Ronald H. , Sijbrands Eric J. G. , Kompanje Erwin J. O. , Girbes Armand R. J. , Barberan Jose , Varona Jose Felipe , Villares Paula , van der Horst Iwan C. C. , Xu Minnan , Celi Leo Anthony , van Bussel Bas C. T. , Borrat Xavier 
Published: June 2023

AbstractSharing healthcare data is increasingly essential for developing data-driven improvements in patient care at the Intensive Care Unit (ICU). However, it is also very challenging under the strict privacy legislation of the European Union (EU). Therefore, we explored four successful open ICU healthcare databases to determine how open healthcare data can be shared appropriately in the EU. A questionnaire was constructed based on the Delphi method. Then, follow-up questions were discussed with experts from the four databases. These experts encountered similar challenges and regarded ethical and legal aspects to be the most challenging. Based on the approaches of the databases, expert opinion, and literature research, we outline four distinct approaches to openly sharing healthcare data, each with varying implications regarding data security, ease of use, sustainability, and implementability. Ultimately, we formulate seven recommendations for sharing open healthcare data to guide future initiatives in sharing open healthcare data to improve patient care and advance healthcare.
Plot-level estimates of aboveground biomass and soil organic carbon stocks from Nepal’s forest inventory
Authors: Khanal Shiva , Boer Matthias M. 
Published: June 2023

AbstractGiven the contribution of deforestation and forest degradation to the global carbon cycle, forest resources are critical to mitigating the global climate change effects. Improved forest monitoring across different biomes is important to understand forest dynamics better and improve global projections of future atmospheric CO2 concentration. Better quantification of the forest carbon cycle advances scientific understanding and informs global negotiations about carbon emissions reduction. High-quality estimates of forest carbon stocks are currently scarce in many developing countries. Here, we present the most comprehensive georeferenced data set to date of plot-level forest carbon estimates for Nepal. Based on field observations from Nepal’s national forest inventory of 2010–2014; the data set includes estimates for two major forest carbon pools, aboveground biomass (AGB) and soil organic carbon (SOC) stocks from 2,009 and 1,156 inventory plots, respectively. The dataset fills an important knowledge gap about forest carbon stocks in the Central Himalayas, a region with highly heterogeneous environmental conditions and rich biodiversity that is poorly represented in existing global estimates of forest carbon.
A curated gene and biological system annotation of adverse outcome pathways related to human health
Authors: Saarimäki Laura Aliisa , Fratello Michele , Pavel Alisa , Korpilähde Seela , Leppänen Jenni , Serra Angela , Greco Dario 
Published: June 2023

AbstractAdverse outcome pathways (AOPs) are emerging as a central framework in modern toxicology and other fields in biomedicine. They serve as an extension of pathway-based concepts by depicting biological mechanisms as causally linked sequences of key events (KEs) from a molecular initiating event (MIE) to an adverse outcome. AOPs guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation. While AOPs model the systemic mechanisms at various levels of biological organisation, toxicogenomics provides the means to study the molecular mechanisms of chemical exposures. Systematic integration of these two concepts would improve the application of AOP-based knowledge while also supporting the interpretation of complex omics data. Hence, we established this link through rigorous curation of molecular annotations for the KEs of human relevant AOPs. We further expanded and consolidated the annotations of the biological context of KEs. These curated annotations pave the way to embed AOPs in molecular data interpretation, facilitating the emergence of new knowledge in biomedicine.
The sequence of the repetitive motif influences the frequency of multistep mutations in Short Tandem Repeats
Authors: Antão-Sousa Sofia , Pinto Nádia , Rende Pablo , Amorim António , Gusmão Leonor 
Published: June 2023

AbstractMicrosatellites, or Short Tandem Repeats (STRs), are subject to frequent length mutations that involve the loss or gain of an integer number of repeats. This work aimed to investigate the correlation between STRs’ specific repetitive motif composition and mutational dynamics, specifically the occurrence of single- or multistep mutations. Allelic transmission data, comprising 323,818 allele transfers and 1,297 mutations, were gathered for 35 Y-chromosomal STRs with simple structure. Six structure groups were established: ATT, CTT, TCTA/GATA, GAAA/CTTT, CTTTT, and AGAGAT, according to the repetitive motif present in the DNA leading strand of the markers. Results show that the occurrence of multistep mutations varies significantly among groups of markers defined by the repetitive motif. The group of markers with the highest frequency of multistep mutations was the one with repetitive motif CTTTT (25% of the detected mutations) and the lowest frequency corresponding to the group with repetitive motifs TCTA/GATA (0.93%). Statistically significant differences (α = 0.05) were found between groups with repetitive motifs with different lengths, as is the case of TCTA/GATA and ATT (p = 0.0168), CTT (p < 0.0001) and CTTTT (p < 0.0001), as well as between GAAA/CTTT and CTTTT (p = 0.0102). The same occurred between the two tetrameric groups GAAA/CTTT and TCTA/GATA (p < 0.0001) – the first showing 5.7 times more multistep mutations than the second. When considering the number of repeats of the mutated paternal alleles, statistically significant differences were found for alleles with 10 or 12 repeats, between GATA and ATT structure groups. These results, which demonstrate the heterogeneity of mutational dynamics across repeat motifs, have implications in the fields of population genetics, epidemiology, or phylogeography, and whenever STR mutation models are used in evolutionary studies in general.
Multiobjective optimization to assess dengue control costs using a climate-dependent epidemiological model
Authors: de Vasconcelos Amália Soares Vieira , de Lima Josenildo Silva , Cardoso Rodrigo Tomás Nogueira 
Published: June 2023

AbstractArboviruses, diseases transmitted by arthropods, have become a significant challenge for public health managers. The World Health Organization highlights dengue as responsible for millions of infections worldwide annually. As there is no specific treatment for the disease and no free-of-charge vaccine for mass use in Brazil, the best option is the measures to combat the vector, the Aedes aegypti mosquito. Therefore, we proposed an epidemiological model dependent on temperature, precipitation, and humidity, considering symptomatic and asymptomatic dengue infections. Through computer simulations, we aimed to minimize the amount of insecticides and the social cost demanded to treat patients. We proposed a case study in which our model is fitted with real data from symptomatic dengue-infected humans in an epidemic year in a Brazilian city. Our multiobjective optimization model considers an additional control using larvicide, adulticide, and ultra-low volume spraying. The work’s main contribution is studying the monetary cost of the actions to combat the vector demand versus the hospital cost per confirmed infected, comparing approaches with and without additional control. Results showed that the additional vector control measures are cheaper than the hospital treatment without the vector control would be.
Synthesis, characterization and evaluation of anti-arthritic and anti-inflammatory potential of curcumin loaded chitosan nanoparticles
Authors: Asif Hafiz Muhammad , Zafar Farah , Ahmad Khalil , Iqbal Amjad , Shaheen Ghazala , Ansari Khalil Ahmad , Rana Sehrish , Zahid Rabia , Ghaffar Saira 
Published: June 2023

AbstractCurcumin is a phytochemical isolated from the dried rhizome of Curcuma longa L. family Zingiberaceae which possesses versatile biological activities and has hydrophobic properties. The current study was conducted to fabricate, and optimize curcumin loaded chitosan and Sodium tripolyphosphate (STPP) nanoparticles (NPs) to improve the bioavailability of curcumin. NPs were fabricated employing the Ionic gelation method. Four formulations were developed based on the selected variables like STPP and chitosan concentration, rotations per minute (rpm), temperature, and pH of chitosan solution. NPs were characterized for morphology, drug-polymer compatibility, yield, particle size, encapsulation efficiency, release behavior, anti-inflammatory and anti-arthritic activity compared to curcumin and standard drug. Fourier transform infrared spectroscopy (FTIR) shows nanoparticle compatibility. The maximum yield was 60%. Entrapment efficiency ranged from 45 to 65%. Curcumin NPs and standard drug 600 µg/ml shows 59% and 70% anti-inflammatory activity by HRB membrane stabilization method respectively which are greater than curcumin alone whereas anti-arthritic activity by protein denaturation method which is also comparable to standard drug and greater than curcumin was 66 and 70% respectively. Statistical analysis shows the mean significant difference at p ≤ 0.05. The study concluded that curcumin-loaded chitosan and STPP NPs formulated successfully by the Ionic gelation method, which increased curcumin absorption leading to a reduced dosing rate and improved patient compliance.
Uniquely low stable iron isotopic signatures in deep marine sediments caused by Rayleigh distillation
Authors: Köster Male , Staubwasser Michael , Meixner Anette , Kasemann Simone A. , Manners Hayley R. , Morono Yuki , Inagaki Fumio , Heuer Verena B. , Kasten Sabine , Henkel Susann 
Published: June 2023

AbstractDissimilatory iron reduction (DIR) is suggested to be one of the earliest forms of microbial respiration. It plays an important role in the biogeochemical cycling of iron in modern and ancient sediments. Since microbial iron cycling is typically accompanied by iron isotope fractionation, stable iron isotopes are used as tracer for biological activity. Here we present iron isotope data for dissolved and sequentially extracted sedimentary iron pools from deep and hot subseafloor sediments retrieved in the Nankai Trough off Japan. Dissolved iron (Fe(II)aq) is isotopically light throughout the ferruginous sediment interval but some samples have exceptionally light isotope values. Such light values have never been reported in natural marine environments and cannot be solely attributed to DIR. We show that the light isotope values are best explained by a Rayleigh distillation model where Fe(II)aq is continuously removed from the pore water by adsorption onto iron (oxyhydr)oxide surfaces. While the microbially mediated Fe(II)aq release has ceased due to an increase in temperature beyond the threshold of mesophilic microorganisms, the abiotic adsorptive Fe(II)aq removal continued, leading to uniquely light isotope values. These findings have important implications for the interpretation of dissolved iron isotope data especially in deep subseafloor sediments.
Low length-for-age Z-score within 1 month after birth predicts hyperdynamic circulation at the age of 21 years in rural Malawi
Authors: Penninkangas Roosa-Maria , Choudhary Manoj Kumar , Mangani Charles , Maleta Kenneth , Teivaanmäki Tiina , Niemelä Onni , Ashorn Per , Ashorn Ulla , Pörsti Ilkka 
Published: June 2023

AbstractLow birth weight predisposes to the development of hypertension in middle- and high-income countries. We examined the relation of early life length-for-age score (Z-score) on cardiovascular function in young adults in Malawi, a low-income country. Capture of supine, seated, and standing brachial pulse waveforms (Mobil-O-Graph) were performed in 223 females and 152 males (mean age 21 years), and analyzed according to the length-for-age Z-score tertiles during the first month of life. Plasma LDL cholesterol in young adulthood was slightly lower in the lowest versus highest tertile. Otherwise, blood hemoglobin and plasma chemistry were similar in all tertiles. Irrespective of posture, blood pressure, forward and backward wave amplitudes, and pulse wave velocity were corresponding in all tertiles. In the three postures, the lowest tertile presented with 4.5% lower systemic vascular resistance than the highest tertile (p = 0.005), and 4.4% and 5.5% higher cardiac output than the middle and highest tertiles, respectively (p < 0.01). Left cardiac work was 6.8% and 6.9% higher in the lowest tertile than in the middle and highest tertiles, respectively (p < 0.01). To conclude, in a low-income environment, low length-for-age Z-score after birth predicted hyperdynamic circulation at 21 years of age without changes in blood pressure and metabolic variables.
Imaging and identification of single nanoplastic particles and agglomerates
Authors: Shorny Ambika , Steiner Fritz , Hörner Helmut , Skoff Sarah M. 
Published: June 2023

AbstractPollution by nanoplastic is a growing environmental and health concern. Currently the extent of nanoplastic in the environment can only be cumbersomely and indirectly estimated but not measured. To be able to quantify the extent of the problem, detection methods that can identify nanoplastic particles that are smaller than 1 $$\mu$$
μ
m are critically needed. Here, we employ surface-enhanced Raman scattering (SERS) to image and identify single nanoplastic particles down to 100 nm in size. We can differentiate between single particles and agglomerates and our method allows an improvement in detection speed of $$10^{7}$$

10
7

compared to state-of-the art surface-enhanced Raman imaging. Being able to resolve single particles allows to measure the SERS enhancement factor on individual nanoplastic particles instead of averaging over a concentration without spatial information. Our results thus contribute to the better understanding and employment of SERS for nanoplastic detection and present an important step for the development of future sensors.
Identification of hub genes and potential ceRNA networks of diabetic cardiomyopathy
Authors: Hou Jun , Liang Wan Yi , Xiong Shiqiang , Long Pan , Yue Tian , Wen Xudong , Wang Tianchen , Deng Haoyu 
Published: June 2023

AbstractDiabetic cardiomyopathy (DCM), a common complication of diabetes, is defined as ventricular dysfunction in the absence of underlying heart disease. Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), play a crucial role in the development of DCM. Weighted Gene Co-Expression Network Analysis (WGCNA) was used to identify key modules in DCM-related pathways. DCM-related miRNA-mRNA network and DCM-related ceRNA network were constructed by miRNA-seq to identify hub genes in these modules. We identified five hub genes that are associated with the onset of DCM, including Troponin C1 (Tnnc1), Phospholamban (Pln), Fatty acid binding proteins 3 (Fabp3), Popeye domain containing 2 (Popdc2), and Tripartite Motif-containing Protein 63 (Trim63). miRNAs that target the hub genes were mainly involved in TGF-β and Wnt signaling pathways. GO BP enrichment analysis found these miRNAs were involved in the signaling of TGF-β and glucose homeostasis. Q-PCR results found the gene expressions of Pln, Fabp3, Trim63, Tnnc1, and Popdc2 were significantly increased in DCM. Our study identified five hub genes (Tnnc1, Pln, Fabp3, Popdc2, Trim63) whose associated ceRNA networks are responsible for the onset of DCM.
Genetic diversity of Helicobacter pylori type IV secretion system cagI and cagN genes and their association with clinical diseases
Authors: Azizimoghaddam Yasaman , Kermanpour Sadaf , Mirzaei Nasrin , Houri Hamidreza , Nabavi-Rad Ali , Asadzadeh Aghdaei Hamid , Yadegar Abbas , Zali Mohammad Reza 
Published: June 2023

AbstractA number ofcagPAI genes in theHelicobacter pylorigenome are considered the most evolved genes under a diversifying selection and evolutionary pressure. Among them,cagI andcagN are described as a part of the two different-operon ofcagPAI that are involved in the T4SS machinery, but the definite association of these factors with clinical manifestations is still unclear. A total of 70H. pyloriisolates were obtained from different gastroduodenal patients. All isolates were examined for the presence of primaryH. pylorivirulence genes by PCR analysis. Direct DNA sequence analysis was performed for thecagIandcagNgenes. The results were compared with the reference strain. ThecagI,cagN,cagA,cagL,vacAs1m1,vacAs1m2,vacAs2m2,babA2,sabA, anddupAgenotypes were detected in 80, 91.4, 84, 91.4, 32.8, 42.8, 24.4, 97.1, 84.3, and 84.3% of the total isolates, respectively. The most variable codon usage incagIwas observed at residues 20–25, 55–60, 94, 181–199, 213–221, 241–268, and 319–320, while the most variable codon usage in CagN hypervariable motif (CagNHM) was observed at residues 53 to 63. Sequencing data analysis ofcagNrevealed a hypothetical hexapeptide motif (EAKDEN/K) in residues of 278–283 among sixH. pyloriisolates, which needs further studies to evaluate its putative function. The present study demonstrated a high prevalence ofcagIandcagNgenes among IranianH. pyloriisolates with gastroduodenal diseases. Furthermore, no significant correlation betweencagIandcagNvariants and clinical diseases was observed in the present study. However, all patients had a high prevalence ofcagPAI genes includingcagI,cagN,cagA, andcagL, which indicates more potential role of these genes in disease outcome.
Infant visual preference for the mother’s face and longitudinal associations with emotional reactivity in the first year of life
Authors: Rigato Silvia , Stets Manuela , Charalambous Sophia , Dvergsdal Henrik , Holmboe Karla 
Published: June 2023

AbstractPast research has focused on infants’ visual preference for the mother’s face, however it is still unknown how these responses change over time and what factors associate with such changes. A longitudinal study (N ~ 60) was conducted to investigate the trajectories of infant visual preference for the mother’s face and how these are related to the development of emotional reactivity in the first year of life. Two face stimuli (i.e., the infant’s mother and a consistent stranger face) were used in a visual preference task at 2 weeks, 4, 6, and 9 months of age. At each time point, mothers were asked to complete a measure of infant temperament via standardised questionnaires. Our results show that while at 2 weeks, 4 months and 9 months of age infants looked equally at both faces, infants at 6 months looked significantly longer at their mother’s face. We also observed prospective associations with emotional reactivity variables so that infants who looked longer at the mother’s face at 6 months showed higher falling reactivity, i.e. a better ability to recover from distress, at 9 months. We discuss these findings in light of the roles that both infant development and the caregiver play in emerging emotion regulation capacities during the first year of life.