bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purine nucleotide depletion prompts cell migration by stimulating the serine synthesis pathway
Authors: Soflaee Mona Hoseini , Kesavan Rushendhiran , Sahu Umakant , Tasdogan Alpaslan , Villa Elodie , Djabari Zied , Cai Feng , Tran Diem H. , Vu Hieu S. , Ali Eunus S. , Rion Halie , O’Hara Brendan P. , Kelekar Sherwin , Hallett James Hughes , Martin Misty , Mathews Thomas P. , Gao Peng , Asara John M. , Manning Brendan D. , Ben-Sahra Issam , Hoxhaj Gerta 
Published: May 2022

AbstractPurine nucleotides are necessary for various biological processes related to cell proliferation. Despite their importance in DNA and RNA synthesis, cellular signaling, and energy-dependent reactions, the impact of changes in cellular purine levels on cell physiology remains poorly understood. Here, we find that purine depletion stimulates cell migration, despite effective reduction in cell proliferation. Blocking purine synthesis triggers a shunt of glycolytic carbon into the serine synthesis pathway, which is required for the induction of cell migration upon purine depletion. The stimulation of cell migration upon a reduction in intracellular purines required one-carbon metabolism downstream of de novo serine synthesis. Decreased purine abundance and the subsequent increase in serine synthesis triggers an epithelial-mesenchymal transition (EMT) and, in cancer models, promotes metastatic colonization. Thus, reducing the available pool of intracellular purines re-routes metabolic flux from glycolysis into de novo serine synthesis, a metabolic change that stimulates a program of cell migration.
High capacity topological coding based on nested vortex knots and links
Authors: Kong Ling-Jun , Zhang Weixuan , Li Peng , Guo Xuyue , Zhang Jingfeng , Zhang Furong , Zhao Jianlin , Zhang Xiangdong 
Published: May 2022

AbstractOptical knots and links have attracted great attention because of their exotic topological characteristics. Recent investigations have shown that the information encoding based on optical knots could possess robust features against external perturbations. However, as a superior coding scheme, it is also necessary to achieve a high capacity, which is hard to be fulfilled by existing knot-carriers owing to the limit number of associated topological invariants. Thus, how to realize the knot-based information coding with a high capacity is a key problem to be solved. Here, we create a type of nested vortex knot, and show that it can be used to fulfill the robust information coding with a high capacity assisted by a large number of intrinsic topological invariants. In experiments, we design and fabricate metasurface holograms to generate light fields sustaining different kinds of nested vortex links. Furthermore, we verify the feasibility of the high-capacity coding scheme based on those topological optical knots. Our work opens another way to realize the robust and high-capacity optical coding, which may have useful impacts on the field of information transfer and storage.
Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists
Authors: Katti Sachin S. , Krieger Inna V. , Ann Jihyae , Lee Jeewoo , Sacchettini James C. , Igumenova Tatyana I. 
Published: May 2022

AbstractDiacylglycerol (DAG) is a versatile lipid whose 1,2-sn-stereoisomer serves both as second messenger in signal transduction pathways that control vital cellular processes, and as metabolic precursor for downstream signaling lipids such as phosphatidic acid. Effector proteins translocate to available DAG pools in the membranes by using conserved homology 1 (C1) domains as DAG-sensing modules. Yet, how C1 domains recognize and capture DAG in the complex environment of a biological membrane has remained unresolved for the 40 years since the discovery of Protein Kinase C (PKC) as the first member of the DAG effector cohort. Herein, we report the high-resolution crystal structures of a C1 domain (C1B from PKCδ) complexed to DAG and to each of four potent PKC agonists that produce different biological readouts and that command intense therapeutic interest. This structural information details the mechanisms of stereospecific recognition of DAG by the C1 domains, the functional properties of the lipid-binding site, and the identities of the key residues required for the recognition and capture of DAG and exogenous agonists. Moreover, the structures of the five C1 domain complexes provide the high-resolution guides for the design of agents that modulate the activities of DAG effector proteins.
A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs
Authors: Shue Yan Ting , Drainas Alexandros P. , Li Nancy Yanzhe , Pearsall Sarah M. , Morgan Derrick , Sinnott-Armstrong Nasa , Hipkins Susan Q. , Coles Garry L. , Lim Jing Shan , Oro Anthony E. , Simpson Kathryn L. , Dive Caroline , Sage Julien 
Published: May 2022

AbstractThe Notch pathway is a conserved cell-cell communication pathway that controls cell fate decisions. Here we sought to determine how Notch pathway activation inhibits the neuroendocrine cell fate in the lungs, an archetypal process for cell fate decisions orchestrated by Notch signaling that has remained poorly understood at the molecular level. Using intratumoral heterogeneity in small-cell lung cancer as a tractable model system, we uncovered a role for the transcriptional regulators REST and YAP as promoters of the neuroendocrine to non-neuroendocrine transition. We further identified the specific neuroendocrine gene programs repressed by REST downstream of Notch in this process. Importantly, we validated the importance of REST and YAP in neuroendocrine to non-neuroendocrine cell fate switches in both developmental and tissue repair processes in the lungs. Altogether, these experiments identify conserved roles for REST and YAP in Notch-driven inhibition of the neuroendocrine cell fate in embryonic lungs, adult lungs, and lung cancer.
Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays
Authors: Chen Yahong , Yang Chaoyong , Zhu Zhi , Sun Wei 
Published: May 2022

AbstractWhile DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.
Quantum-limited determination of refractive index difference by means of entanglement
Authors: Reisner M. , Mazeas F. , Dauliat R. , Leconte B. , Aktas D. , Cannon R. , Roy P. , Jamier R. , Sauder G. , Kaiser F. , Tanzilli S. , Labonté L. 
Published: May 2022

AbstractShaping single-mode operation in high-power fibers requires a precise knowledge of the gain-medium optical properties. This requires precise measurements of the refractive index differences (Δn) between the core and the cladding of the fiber. We exploit a quantum optical method based on low-coherence Hong-Ou-Mandel interferometry to perform practical measurements of the refractive index difference using broadband energy-time entangled photons. The precision enhancement reached with this method is benchmarked with a classical method based on single photon interferometry. We show in classical regime an improvement by an order of magnitude of the precision compared to already reported classical methods. Strikingly, in the quantum regime, we demonstrate an extra factor of 4 on the precision enhancement, exhibiting a state-of-the-art Δnprecision of 6 × 10−7. This work sets the quantum photonics metrology as a powerful characterization tool that should enable a faster and reliable design of materials dedicated to light amplification.
Global cycling and climate effects of aeolian dust controlled by biological soil crusts
Authors: Rodriguez-Caballero E. , Stanelle T. , Egerer S. , Cheng Y. , Su H. , Canton Y. , Belnap J. , Andreae M. O. , Tegen I. , Reick C. H. , Pöschl U. , Weber B. 
Published: May 2022

AbstractBiological soil crusts (biocrusts) cover ~12% of the global land surface. They are formed by an intimate association between soil particles, photoautotrophic and heterotrophic organisms, and they effectively stabilize the soil surface of drylands. Quantitative information on the impact of biocrusts on the global cycling and climate effects of aeolian dust, however, is not available. Here, we combine the currently limited experimental data with a global climate model to investigate the effects of biocrusts on regional and global dust cycling under current and future conditions. We estimate that biocrusts reduce the global atmospheric dust emissions by ~60%, preventing the release of ~0.7 Pg dust per year. Until 2070, biocrust coverage is expected to be severely reduced by climate change and land-use intensification. The biocrust loss will cause an increased dust burden, leading to a reduction of the global radiation budget of around 0.12 to 0.22 W m−2, corresponding to about 50% of the total direct forcing of anthropogenic aerosols. This biocrust control on dust cycling and its climate impacts have important implications for human health, biogeochemical cycling and the functioning of the ecosystems, and thus should be considered in the modelling, mitigation and management of global change.
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration
Authors: Priya Sambhawa , Burns Michael B. , Ward Tonya , Mars Ruben A. T. , Adamowicz Beth , Lock Eric F. , Kashyap Purna C. , Knights Dan , Blekhman Ran 
Published: May 2022

AbstractWhile gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such asStreptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene–microbiome associations that may influence disease outcomes.
Simulated carbon K edge spectral database of organic molecules
Authors: Shibata Kiyou , Kikumasa Kakeru , Kiyohara Shin , Mizoguchi Teruyasu 
Published: May 2022

AbstractHere we provide a database of simulated carbon K (C-K) edge core loss spectra of 117,340 symmetrically unique sites in 22,155 molecules with no more than eight non-hydrogen atoms (C, O, N, and F). Our database contains C-K edge spectra of each carbon site and those of molecules along with their excitation energies. Our database is useful for analyzing experimental spectrum and conducting spectrum informatics on organic materials.
A global inventory of animal diversity measured in different grazing treatments
Authors: Barber-Cross Tianna , Filazzola Alessandro , Brown Charlotte , Dettlaff Margarete A. , Batbaatar Amgaa , Grenke Jessica S. J. , Peetoom Heida Isaac , Cahill James F. 
Published: May 2022

AbstractGrazing by wild and domesticated grazers occurs within many terrestrial ecosystems worldwide, with positive and negative impacts on biodiversity. Management of grazed lands in support of biological conservation could benefit from a compiled dataset of animal biodiversity within and adjacent to grazed sites. In this database, we have assembled data from the peer-reviewed literature that included all forms of grazing, co-occurring species, and site information. We reviewed 3,489 published articles and found 245 studies in 41 countries that surveyed animal biodiversity co-occurring with grazers. We extracted 16,105 observations of animal surveys for over 1,200 species in all terrestrial ecosystems and on all continents except Antarctica. We then compiled 28 different grazing variables that focus on management systems, assemblages of grazer species, ecosystem characteristics, and survey type. Our database provides the most comprehensive summary of animal biodiversity patterns that co-occur with wild and domesticated grazers. This database could be used in future conservation initiatives and grazing management to enhance the prolonged maintenance of ecosystems and ecosystem services.
Cloud-based applications for accessing satellite Earth observations to support malaria early warning
Authors: Wimberly Michael C. , Nekorchuk Dawn M. , Kankanala Ramcharan R. 
Published: May 2022

AbstractMalaria epidemics can be triggered by fluctuations in temperature and precipitation that influence vector mosquitoes and the malaria parasite. Identifying and monitoring environmental risk factors can thus provide early warning of future outbreaks. Satellite Earth observations provide relevant measurements, but obtaining these data requires substantial expertise, computational resources, and internet bandwidth. To support malaria forecasting in Ethiopia, we developed software for Retrieving Environmental Analytics for Climate and Health (REACH). REACH is a cloud-based application for accessing data on land surface temperature, spectral indices, and precipitation using the Google Earth Engine (GEE) platform. REACH can be implemented using the GEE code editor and JavaScript API, as a standalone web app, or as package with the Python API. Users provide a date range and data for 852 districts in Ethiopia are automatically summarized and downloaded as tables. REACH was successfully used in Ethiopia to support a pilot malaria early warning project in the Amhara region. The software can be extended to new locations and modified to access other environmental datasets through GEE.
Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
Authors: Ali Omar , Ramsubhag Adesh , Daniram Benn Jr. Ramnarine Stephen , Jayaraman Jayaraj 
Published: May 2022

AbstractExtracts of Ascophyllum nodosum are commonly used as commercial biostimulants in crop production. To further understand the seaweed extract-induced phenomena in plants, a transcriptomic study was conducted. RNA-seq differential gene expression analysis of tomato plants treated with a commercial A. nodosum extract formulation (Stimplex) revealed the up-regulation of 635 and down-regulation of 456 genes. Ontology enrichment analysis showed three gene categories were augmented, including biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed that the extract had a strong influence on the expression of genes involved in carbon fixation, secondary metabolism, MAPK-signalling, plant hormone signal transduction, glutathione metabolism, phenylpropanoid and stilbenoid metabolism, and plant-pathogen interactions. qRT-PCR validation analysis using 15 genes established a strong correlation with the RNA sequencing results. The activities of defence enzymes were also significantly enhanced by seaweed extract treatment. Furthermore, AN-SWE treated tomato plants had significantly higher chlorophyll and growth hormone content and showed improved plant growth parameters and nutrient profiles than the control. It is postulated that seaweed extract-induced gene regulation was responsible for favourable plant responses that enabled better growth and tolerance to stress conditions. This study provides evidence at the transcriptomic level for the positive effects of foliar application of the Ascophyllum nodosum extract (Stimplex) observed in treated tomato plants.
Immunological profiles of the breast cancer microenvironment represented by tumor-infiltrating lymphocytes and PD-L1 expression
Authors: Hanamura Toru , Kitano Shigehisa , Kagamu Hiroshi , Yamashita Makiko , Terao Mayako , Tsuda Banri , Okamura Takuho , Kumaki Nobue , Hozumi Katsuto , Harada Naoki , Iwamoto Takayuki , Honda Chikako , Kurozumi Sasagu , Niikura Naoki 
Published: May 2022

AbstractTumor-infiltrating lymphocytes (TILs) and programmed cell death 1 ligand 1 (PD-L1) are established prognostic and predictive biomarkers for certain breast cancer subsets. However, their association with the immune response complexity is not fully understood. Therefore, we analyzed the association between the immune cell fractions in breast cancer tissues and histologically assessed TIL (hTIL) and PD-L1 (hPD-L1). Forty-five tumor and eighteen blood samples were collected from patients with breast cancer. Total leukocyte counts, frequency of 11 immune cell populations, and PD-L1 expression in each cell fraction were evaluated by flow cytometry. TILs and PD-L1 were assessed by hematoxylin and eosin staining and immunohistochemistry, respectively. A higher hTIL score showed association with increased leukocyte infiltration, higher CD4+ and CD8+ T cell proportions, and lower natural killer and natural killer T cell proportions. PD-L1 was highly expressed in nonclassical monocytes, monocyte/macrophages, myeloid-derived suppressor cells, myeloid dendritic cells, dendritic cells, and other lineages in tumors. hPD-L1 positivity reflected PD-L1 expression accurately in these fractions, as well as increased leukocyte infiltration in tumors. These results indicate that hTILs reflect differences in the immune responses in the tumor microenvironment, and certain immune cell fractions are favorably expressed in the PD-L1 pathway in breast cancer microenvironments.
Inducing respiratory complex I impairment elicits an increase in PGC1α in ovarian cancer
Authors: De Luise Monica , Sollazzo Manuela , Lama Eleonora , Coadă Camelia Alexandra , Bressi Licia , Iorio Maria , Cavina Beatrice , D’Angelo Luigi , Milioni Sara , Marchio Lorena , Miglietta Stefano , Coluccelli Sara , Tedesco Greta , Ghelli Anna , Lemma Silvia , Perrone Anna Myriam , Kurelac Ivana , Iommarini Luisa , Porcelli Anna Maria , Gasparre Giuseppe 
Published: May 2022

AbstractAnticancer strategies aimed at inhibiting Complex I of the mitochondrial respiratory chain are increasingly being attempted in solid tumors, as functional oxidative phosphorylation is vital for cancer cells. Using ovarian cancer as a model, we show that a compensatory response to an energy crisis induced by Complex I genetic ablation or pharmacological inhibition is an increase in the mitochondrial biogenesis master regulator PGC1α, a pleiotropic coactivator of transcription regulating diverse biological processes within the cell. We associate this compensatory response to the increase in PGC1α target gene expression, setting the basis for the comprehension of the molecular pathways triggered by Complex I inhibition that may need attention as drawbacks before these approaches are implemented in ovarian cancer care.
Individualizing deep dynamic models for psychological resilience data
Authors: Köber Göran , Pooseh Shakoor , Engen Haakon , Chmitorz Andrea , Kampa Miriam , Schick Anita , Sebastian Alexandra , Tüscher Oliver , Wessa Michèle , Yuen Kenneth S. L. , Walter Henrik , Kalisch Raffael , Timmer Jens , Binder Harald 
Published: May 2022

AbstractDeep learning approaches can uncover complex patterns in data. In particular, variational autoencoders achieve this by a non-linear mapping of data into a low-dimensional latent space. Motivated by an application to psychological resilience in the Mainz Resilience Project, which features intermittent longitudinal measurements of stressors and mental health, we propose an approach for individualized, dynamic modeling in this latent space. Specifically, we utilize ordinary differential equations (ODEs) and develop a novel technique for obtaining person-specific ODE parameters even in settings with a rather small number of individuals and observations, incomplete data, and a differing number of observations per individual. This technique allows us to subsequently investigate individual reactions to stimuli, such as the mental health impact of stressors. A potentially large number of baseline characteristics can then be linked to this individual response by regularized regression, e.g., for identifying resilience factors. Thus, our new method provides a way of connecting different kinds of complex longitudinal and baseline measures via individualized, dynamic models. The promising results obtained in the exemplary resilience application indicate that our proposal for dynamic deep learning might also be more generally useful for other application domains.
New approach to prepare cytocompatible 3D scaffolds via the combination of sodium hyaluronate and colloidal particles of conductive polymers
Authors: Truong Thanh Huong , Musilová Lenka , Kašpárková Věra , Jasenská Daniela , Ponížil Petr , Minařík Antonín , Korábková Eva , Münster Lukáš , Hanulíková Barbora , Mráček Aleš , Rejmontová Petra , Humpolíček Petr 
Published: May 2022

AbstractBio-inspired conductive scaffolds composed of sodium hyaluronate containing a colloidal dispersion of water-miscible polyaniline or polypyrrole particles (concentrations of 0.108, 0.054 and 0.036% w/w) were manufactured. For this purpose, either crosslinking with N-(3-dimethylaminopropyl-N-ethylcarbodiimide hydrochloride and N-hydroxysuccinimid or a freeze-thawing process in the presence of poly(vinylalcohol) was used. The scaffolds comprised interconnected pores with prevailing porosity values of ~ 30% and pore sizes enabling the accommodation of cells. A swelling capacity of 92–97% without any sign of disintegration was typical for all samples. The elasticity modulus depended on the composition of the scaffolds, with the highest value of ~ 50 kPa obtained for the sample containing the highest content of polypyrrole particles. The scaffolds did not possess cytotoxicity and allowed cell adhesion and growth on the surface. Using the in vivo-mimicking conditions in a bioreactor, cells were also able to grow into the structure of the scaffolds. The technique of scaffold preparation used here thus overcomes the limitations of conductive polymers (e.g. poor solubility in an aqueous environment, and limited miscibility with other hydrophilic polymer matrices) and moreover leads to the preparation of cytocompatible scaffolds with potentially cell-instructive properties, which may be of advantage in the healing of damaged electro-sensitive tissues.