bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of air pollution on the transcriptomics of the immune response to respiratory infection
Authors: Croft Daniel P. , Burton David S. , Nagel David J. , Bhattacharya Soumyaroop , Falsey Ann R. , Georas Steve N. , Hopke Philip K. , Johnston Carl J. , Kottmann R. Matthew , Litonjua Augusto A. , Mariani Thomas J. , Rich David Q. , Thevenet-Morrison Kelly , Thurston Sally W. , Utell Mark J. , McCall Matthew N. 
Published: September 2021

AbstractCombustion related particulate matter air pollution (PM) is associated with an increased risk of respiratory infections in adults. The exact mechanism underlying this association has not been determined. We hypothesized that increased concentrations of combustion related PM would result in dysregulation of the innate immune system. This epidemiological study includes 111 adult patients hospitalized with respiratory infections who underwent transcriptional analysis of their peripheral blood. We examined the association between gene expression at the time of hospitalization and ambient measurements of particulate air pollutants in the 28 days prior to hospitalization. For each pollutant and time lag, gene-specific linear models adjusting for infection type were fit using LIMMA (Linear Models For Microarray Data), and pathway/gene set analyses were performed using the CAMERA (Correlation Adjusted Mean Rank) program. Comparing patients with viral and/or bacterial infection, the expression patterns associated with air pollution exposure differed. Adjusting for the type of infection, increased concentrations of Delta-C (a marker of biomass smoke) and other PM were associated with upregulation of iron homeostasis and protein folding. Increased concentrations of black carbon (BC) were associated with upregulation of viral related gene pathways and downregulation of pathways related to antigen presentation. The pollutant/pathway associations differed by lag time and by type of infection. This study suggests that the effect of air pollution on the pathogenesis of respiratory infection may be pollutant, timing, and infection specific.
Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid
Authors: Gómez-González Paula J. , Perdigao Joao , Gomes Pedro , Puyen Zully M. , Santos-Lazaro David , Napier Gary , Hibberd Martin L. , Viveiros Miguel , Portugal Isabel , Campino Susana , Phelan Jody E. , Clark Taane G. 
Published: September 2021

AbstractTuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases worldwide. Multidrug and extensively drug-resistant strains are making disease control difficult, and exhausting treatment options. New anti-TB drugs bedaquiline (BDQ), delamanid (DLM) and pretomanid (PTM) have been approved for the treatment of multi-drug resistant TB, but there is increasing resistance to them. Nine genetic loci strongly linked to resistance have been identified (mmpR5, atpE, and pepQ for BDQ; ddn, fgd1, fbiA, fbiB, fbiC, and fbiD for DLM/PTM). Here we investigated the genetic diversity of these loci across >33,000 M. tuberculosis isolates. In addition, epistatic mutations in mmpL5-mmpS5 as well as variants in ndh, implicated for DLM/PTM resistance in M. smegmatis, were explored. Our analysis revealed 1,227 variants across the nine genes, with the majority (78%) present in isolates collected prior to the roll-out of BDQ and DLM/PTM. We identified phylogenetically-related mutations, which are unlikely to be resistance associated, but also high-impact variants such as frameshifts (e.g. in mmpR5, ddn) with likely functional effects, as well as non-synonymous mutations predominantly in MDR-/XDR-TB strains with predicted protein destabilising effects. Overall, our work provides a comprehensive mutational catalogue for BDQ and DLM/PTM associated genes, which will assist with establishing associations with phenotypic resistance; thereby, improving the understanding of the causative mechanisms of resistance for these drugs, leading to better treatment outcomes.
Nano-imaging confirms improved apatite precipitation for high phosphate/silicate ratio bioactive glasses
Authors: Jaimes Altair T. Contreras , Kirste Gloria , de Pablos-Martín Araceli , Selle Susanne , de Souza e Silva Juliana Martins , Massera Jonathan , Karpukhina Natalia , Hill Robert G. , Brauer Delia S. 
Published: September 2021

AbstractBioactive glasses convert to a biomimetic apatite when in contact with physiological solutions; however, the number and type of phases precipitating depends on glass composition and reactivity. This process is typically followed by X-ray diffraction and infrared spectroscopy. Here, we visualise surface mineralisation in a series of sodium-free bioactive glasses, using transmission electron microscopy (TEM) with energy-dispersive X-ray spectroscopy (EDXS) and X-ray nano-computed tomography (nano-CT). In the glasses, the phosphate content was increased while adding stoichiometric amounts of calcium to maintain phosphate in an orthophosphate environment in the glass. Calcium fluoride was added to keep the melting temperature low. TEM brought to light the presence of phosphate clustering and nearly crystalline calcium fluoride environments in the glasses. A combination of analytical methods, including solid-state NMR, shows how with increasing phosphate content in the glass, precipitation of calcium fluoride during immersion is superseded by fluorapatite precipitation. Nano-CT gives insight into bioactive glass particle morphology after immersion, while TEM illustrates how compositional changes in the glass affect microstructure at a sub-micron to nanometre-level.
Cell aging related genes can be used to characterize clinical prognoses and further stratify diffuse gliomas
Authors: Yang Yang , Chen Xin , Sun Jianjun , Chen Suhua , Yang Chenlong , Ma Qianquan , Yang Jun 
Published: September 2021

AbstractIncreasing evidence has indicated that senescent cells are associated with the glioma development. Thus, we aimed to explore the relationship between the cellular senescence gene profile and the clinical prognosis of diffuse glioma. In total, 699 gliomas from The Cancer Genome Atlas (TCGA) dataset were used as the training cohort and 693 gliomas from the Chinese Glioma Genome Atlas (CGGA) dataset were used as the validation cohort. Bioinformatics statistical methods are used to develop the risk signature and to study the prognostic value of the risk signature. We identified a 14-gene risk signature and its risk score was an independent prognostic factor (P < 0.001) in the validation dataset. The risk signature had better prognostic value than traditional factors for the 3- and 5-year survival rate. Importantly, the risk signature could further stratify gliomas in specific subgroups of World Health Organization (WHO) classification by the survival rate. Furthermore, the mRNA levels of genes involved in the cell cycle, cell division and other processes were significantly correlated with the risk score. Our study highlighted a 14-gene risk signature for further stratifying the outcomes of patients with gliomas with definite WHO subgroups. These results indicate the potential clinical implications of cell aging-related genes in gliomas.
Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey
Authors: Sato Masaaki , Inoue Nariaki , Nambu Ryogen , Furuichi Naoki , Imaizumi Tomohito , Ushio Masayuki 
Published: September 2021

AbstractSince the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.
Presence of distinctive microbiome in the first-pass meconium of newborn infants
Authors: Turunen Jenni , Tejesvi Mysore V. , Paalanne Niko , Hekkala Jenni , Lindgren Outi , Kaakinen Mika , Pokka Tytti , Kaisanlahti Anna , Reunanen Justus , Tapiainen Terhi 
Published: September 2021

AbstractWe critically evaluated the fetal microbiome concept in 44 neonates with placenta, amniotic fluid, and first-pass meconium samples. Placental histology showed no signs of inflammation. Meconium samples were more often bacterial culture positive after vaginal delivery. In next-generation sequencing of the bacterial 16S gene, before and after removal of extracellular and PCR contaminant DNA, the median number of reads was low in placenta (48) and amniotic fluid (46) and high in meconium samples (14,556 C-section, 24,860 vaginal). In electron microscopy, meconium samples showed extracellular vesicles. Utilizing the analysis of composition of microbiomes (ANCOM) against water, meconium samples had a higher relative abundance of Firmicutes, Lactobacillus, Streptococcus, and Escherichia-Shigella. Our results did not support the existence of the placenta and amniotic fluid microbiota in healthy pregnancies. The first-pass meconium samples, formed in utero, appeared to harbor a microbiome that may be explained by perinatal colonization or intrauterine colonization via bacterial extracellular vesicles.
New chemical biopsy tool for spatially resolved profiling of human brain tissue in vivo
Authors: Bogusiewicz Joanna , Burlikowska Katarzyna , Łuczykowski Kamil , Jaroch Karol , Birski Marcin , Furtak Jacek , Harat Marek , Pawliszyn Janusz , Bojko Barbara 
Published: September 2021

AbstractIt is extremely challenging to perform chemical analyses of the brain, particularly in humans, due to the restricted access to this organ. Imaging techniques are the primary approach used in clinical practice, but they only provide limited information about brain chemistry. Solid-phase microextraction (SPME) has been presented recently as a chemical biopsy tool for the study of animal brains. The current work demonstrates for the first time the use of SPME for the spatially resolved sampling of the human brain in vivo. Specially designed multi-probe sampling device was used to simultaneously extract metabolites from the white and grey matter of patients undergoing brain tumor biopsies. Samples were collected by inserting the probes along the planned trajectory of the biopsy needle prior to the procedure, which was followed by metabolomic and lipidomic analyses. The results revealed that studied brain structures were predominantly composed of lipids, while the concentration and diversity of detected metabolites was higher in white than in grey matter. Although the small number of participants in this research precluded conclusions of a biological nature, the results highlight the advantages of the proposed SPME approach, as well as disadvantages that should be addressed in future studies.
Experimental evolution supports the potential of neonicotinoid-pyrethroid combination for managing insecticide resistance in malaria vectors
Authors: Zoh Marius Gonse , Bonneville Jean-Marc , Tutagata Jordan , Laporte Frederic , Fodjo Behi K. , Mouhamadou Chouaibou S. , Sadia Christabelle Gba , McBeath Justin , Schmitt Frederic , Horstmann Sebastian , Reynaud Stephane , David Jean-Philippe 
Published: September 2021

AbstractThe introduction of neonicotinoids for managing insecticide resistance in mosquitoes is of high interest as they interact with a biochemical target not previously used in public health. In this concern, Bayer developed a combination of the neonicotinoid clothianidin and the pyrethroid deltamethrin (brand name Fludora Fusion) as a new vector control tool. Although this combination proved to be efficient against pyrethroid-resistant mosquitoes, its ability to prevent the selection of pyrethroid and neonicotinoid resistance alleles was not investigated. In this context, the objective of this work was to study the dynamics and the molecular mechanisms of resistance ofAn. gambiaeto the separated or combined components of this combination. A field-derivedAn. gambiaeline carrying resistance alleles to multiple insecticides at low frequencies was used as a starting for 33 successive generations of controlled selection. Resistance levels to each insecticide and target site mutation frequencies were monitored throughout the selection process. Cross resistance to other public health insecticides were also investigated. RNA-seq was used to compare gene transcription variations and polymorphisms across all lines. This study confirmed the potential of this insecticide combination to impair the selection of resistance as compared to its two separated components. Deltamethrin selection led to the rapid enrichment of the kdr L1014F target-site mutation. Clothianidin selection led to the over-transcription of multiple cytochrome P450s including some showing high homology with those conferring neonicotinoid resistance in other insects. A strong selection signature associated with clothianidin selection was also observed on a P450 gene cluster previously associated with resistance. Within this cluster, the geneCYP6M1showed the highest selection signature together with a transcription profile supporting a role in clothianidin resistance. Modelling the impact of point mutations selected by clothianidin on CYP6M1 protein structure showed that selection retained a protein variant with a modified active site potentially enhancing clothianidin metabolism. In the context of the recent deployment of neonicotinoids for mosquito control and their frequent usage in agriculture, the present study highlights the benefit of combining them with other insecticides for preventing the selection of resistance and sustaining vector control activities.
Boosting proximity spin–orbit coupling in graphene/WSe2 heterostructures via hydrostatic pressure
Authors: Fülöp Bálint , Márffy Albin , Zihlmann Simon , Gmitra Martin , Tóvári Endre , Szentpéteri Bálint , Kedves Máté , Watanabe Kenji , Taniguchi Takashi , Fabian Jaroslav , Schönenberger Christian , Makk Péter , Csonka Szabolcs 
Published: September 2021

AbstractVan der Waals heterostructures composed of multiple few layer crystals allow the engineering of novel materials with predefined properties. As an example, coupling graphene weakly to materials with large spin–orbit coupling (SOC) allows to engineer a sizeable SOC in graphene via proximity effects. The strength of the proximity effect depends on the overlap of the atomic orbitals, therefore, changing the interlayer distance via hydrostatic pressure can be utilized to enhance the interlayer coupling between the layers. In this work, we report measurements on a graphene/WSe2 heterostructure exposed to increasing hydrostatic pressure. A clear transition from weak localization to weak antilocalization is visible as the pressure increases, demonstrating the increase of induced SOC in graphene.
Photoluminescence as a probe of phosphorene properties
Authors: Molas Maciej R. , Macewicz Łukasz , Wieloszyńska Aleksandra , Jakóbczyk Paweł , Wysmołek Andrzej , Bogdanowicz Robert , Jasinski Jacek B. 
Published: September 2021

AbstractHere, we provide a detailed evaluation of photoluminescence (PL) as a comprehensive tool for phosphorene characterization with the emphasis on a prominent quantitative role of PL in providing fingerprint-like features due to its extreme sensitivity to the band structure details, anisotropy, disorder, external fields, etc. Factors such as number of layers, dimensionality, structural and chemical disorder, and environmental factors and their effect on phosphorene’s PL signal are reviewed and discussed. Applications of PL in monitoring phosphorene and its modifications, as well as potential impacts on the fields of chemical and biosensing, nanomedicine, and solar energy harvesting, are also elaborated.
Statistical uncertainty quantification to augment clinical decision support: a first implementation in sleep medicine
Authors: Kang Dae Y. , DeYoung Pamela N. , Tantiongloc Justin , Coleman Todd P. , Owens Robert L. 
Published: September 2021

AbstractMachine learning has the potential to change the practice of medicine, particularly in areas that require pattern recognition (e.g. radiology). Although automated classification is unlikely to be perfect, few modern machine learning tools have the ability to assess their own classification confidence to recognize uncertainty that might need human review. Using automated single-channel sleep staging as a first implementation, we demonstrated that uncertainty information (as quantified using Shannon entropy) can be utilized in a “human in the loop” methodology to promote targeted review of uncertain sleep stage classifications on an epoch-by-epoch basis. Across 20 sleep studies, this feedback methodology proved capable of improving scoring agreement with the gold standard over automated scoring alone (average improvement in Cohen’s Kappa of 0.28), in a fraction of the scoring time compared to full manual review (60% reduction). In summary, our uncertainty-based clinician-in-the-loop framework promotes the improvement of medical classification accuracy/confidence in a cost-effective and economically resourceful manner.
A genotyping assay to determine geographic origin and transmission potential of Plasmodium falciparum malaria cases
Authors: Molina-Cruz Alvaro , Raytselis Nadia , Withers Roxanne , Dwivedi Ankit , Crompton Peter D. , Traore Boubacar , Carpi Giovanna , Silva Joana C. , Barillas-Mury Carolina 
Published: September 2021

AbstractAs countries work towards malaria elimination, it is important to monitor imported cases to prevent reestablishment of local transmission. The Plasmodium falciparum Pfs47 gene has strong geographic population structure, because only those parasites with Pfs47 haplotypes compatible with the mosquito vector species in a given continent are efficiently transmitted. Analysis of 4,971 world-wide Pfs47 sequences identified two SNPs (at 707 and 725 bp) as sufficient to establish the likely continent of origin of P. falciparum isolates. Pfs47 sequences from Africa, Asia, and the New World presented more that 99% frequency of distinct combinations of the SNPs 707 and 725 genotypes. Interestingly, Papua New Guinea Pfs47 sequences have the highest diversity in SNPs 707 and 725. Accurate and reproducible High-Resolution Melting (HRM) assays were developed to genotype Pfs47 SNPs 707 and 725 in laboratory and field samples, to assess the geographic origin and risk of local transmission of imported P. falciparum malaria cases.
Neuronal let-7b-5p acts through the Hippo-YAP pathway in neonatal encephalopathy
Authors: Ponnusamy Vennila , Ip Richard T. H. , Mohamed Moumin A. E. K. , Clarke Paul , Wozniak Eva , Mein Charles , Schwendimann Leslie , Barlas Akif , Chisholm Philippa , Chakkarapani Ela , Michael-Titus Adina T. , Gressens Pierre , Yip Ping K. , Shah Divyen K. 
Published: September 2021

AbstractDespite increasing knowledge on microRNAs, their role in the pathogenesis of neonatal encephalopathy remains to be elucidated. Herein, we identify let-7b-5p as a significant microRNA in neonates with moderate to severe encephalopathy from dried blood spots using next generation sequencing. Validation studies using Reverse Transcription and quantitative Polymerase Chain Reaction on 45 neonates showed that let-7b-5p expression was increased on day 1 in neonates with moderate to severe encephalopathy with unfavourable outcome when compared to those with mild encephalopathy. Mechanistic studies performed on glucose deprived cell cultures and the cerebral cortex of two animal models of perinatal brain injury, namely hypoxic-ischaemic and intrauterine inflammation models confirm that let-7b-5p is associated with the apoptotic Hippo pathway. Significant reduction in neuronal let-7b-5p expression corresponded with activated Hippo pathway, with increased neuronal/nuclear ratio of Yes Associated Protein (YAP) and increased neuronal cleaved caspase-3 expression in both animal models. Similar results were noted for let-7b-5p and YAP expression in glucose-deprived cell cultures. Reduced nuclear YAP with decreased intracellular let-7b-5p correlated with neuronal apoptosis in conditions of metabolic stress. This finding of the Hippo-YAP association with let-7b needs validation in larger cohorts to further our knowledge on let-7b-5p as a biomarker for neonatal encephalopathy.
Spatial frameworks for robust estimation of yield gaps
Authors: Rattalino Edreira Juan I. , Andrade José F. , Cassman Kenneth G. , van Ittersum Martin K. , van Loon Marloes P. , Grassini Patricio 
Published: September 2021

AbstractFood security interventions and policies need reliable estimates of crop production and the scope to enhance production on existing cropland. Here we assess the performance of two widely used ‘top-down’ gridded frameworks (Global Agro-ecological Zones and Agricultural Model Intercomparison and Improvement Project) versus an alternative ‘bottom-up’ approach (Global Yield Gap Atlas). The Global Yield Gap Atlas estimates extra production potential locally for a number of sites representing major breadbaskets and then upscales the results to larger spatial scales. We find that estimates from top-down frameworks are alarmingly unlikely, with estimated potential production being lower than current farm production at some locations. The consequences of using these coarse estimates to predict food security are illustrated by an example for sub-Saharan Africa, where using different approaches would lead to different prognoses about future cereal self-sufficiency. Our study shows that foresight about food security and associated agriculture research priority setting based on yield potential and yield gaps derived from top-down approaches are subject to a high degree of uncertainty and would benefit from incorporating estimates from bottom-up approaches.