bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling
Authors: García-Romero Inmaculada , Nogales Juan , Díaz Eduardo , Santero Eduardo , Floriano Belén 
Published: May 2020

AbstractSphingopyxis granuli strain TFA is an α-proteobacterium that belongs to the sphingomonads, a group of bacteria well-known for its degradative capabilities and oligotrophic metabolism. Strain TFA is the only bacterium in which the mineralisation of the aromatic pollutant tetralin has been completely characterized at biochemical, genetic, and regulatory levels and the first Sphingopyxis characterised as facultative anaerobe. Here we report additional metabolic features of this α-proteobacterium using metabolic modelling and the functional integration of genomic and transcriptomic data. The genome-scale metabolic model (GEM) of strain TFA, which has been manually curated, includes information on 743 genes, 1114 metabolites and 1397 reactions. This represents the largest metabolic model for a member of the Sphingomonadales order thus far. The predictive potential of this model was validated against experimentally calculated growth rates on different carbon sources and under different growth conditions, including both aerobic and anaerobic metabolisms. Moreover, new carbon and nitrogen sources were predicted and experimentally validated. The constructed metabolic model was used as a platform for the incorporation of transcriptomic data, generating a more robust and accurate model. In silico flux analysis under different metabolic scenarios highlighted the key role of the glyoxylate cycle in the central metabolism of strain TFA.
Width identification of transition zone between desert and oasis based on NDVI and TCI
Authors: JI Shuxin , Bai Xuelian , Qiao Rongrong , Wang Lixiang , Chang Xueli 
Published: May 2020

AbstractThe oasis-desert transition zone, the boundary between the desert and oasis, has special significance in maintaining oasis stability and indicating ecosystem health. The width of the boundary is one of the critical indicators to determine the sampling design and restrict findings scaling in the study of the desert oasis transition zone. Buffer analyze and focal analyze were conducted to determine the width among oasis-desert transition zone and oasis artificial sand fixation zone in Hexi corridor China. Focal analyses indicate that TCImax and TCImin can constrain NDVI of trend variation, and the effect increases with the analysis scale. On the same spatial scale, NDVI and TCI have opposite trends and have intersections. The intersection of the sandy desert transition zone is between 30–90 m, and the oasis artificial sand-fixaion zone is between 90–150 m. The width of the sandy desert transition zone is between 220–300 m, and the width increases with the increase of analysis scale. The oasis artificial sand-fixation zone is between 420 and 540 m, which decreases with the increase of the analysis scale. NDVI shows a trend of decreasing from the oasis boundary to the desert, the trend of TCI is different from that of NDVI, showing an increase from the edge of oasis to the interior of desert. The differences in the spatial distribution of NDVI and TCI can be clearly expressed, and different types of transition zones and analysis scales have their own characteristics.
Controllable skyrmion chirality in ferroelectrics
Authors: Tikhonov Yu. , Kondovych S. , Mangeri J. , Pavlenko M. , Baudry L. , Sené A. , Galda A. , Nakhmanson S. , Heinonen O. , Razumnaya A. , Luk’yanchuk I. , Vinokur V. M. 
Published: May 2020

AbstractChirality, an intrinsic handedness, is one of the most intriguing fundamental phenomena in nature. Materials composed of chiral molecules find broad applications in areas ranging from nonlinear optics and spintronics to biology and pharmaceuticals. However, chirality is usually an invariable inherent property of a given material that cannot be easily changed at will. Here, we demonstrate that ferroelectric nanodots support skyrmions the chirality of which can be controlled and switched. We devise protocols for realizing control and efficient manipulations of the different types of skyrmions. Our findings open the route for controlled chirality with potential applications in ferroelectric-based information technologies.
Microglia Dynamics and Interactions with Motoneurons Axotomized After Nerve Injuries Revealed By Two-Photon Imaging
Authors: Rotterman Travis M. , Alvarez Francisco J. 
Published: May 2020

AbstractThe significance of activated microglia around motoneurons axotomized after nerve injuries has been intensely debated. In particular, whether microglia become phagocytic is controversial. To resolve these issues we directly observed microglia behaviors with two-photon microscopy in ex vivo spinal cord slices from CX3CR1-GFP mice complemented with confocal analyses of CD68 protein. Axotomized motoneurons were retrogradely-labeled from muscle before nerve injuries. Microglia behaviors close to axotomized motoneurons greatly differ from those within uninjured motor pools. They develop a phagocytic phenotype as early as 3 days after injury, characterized by frequent phagocytic cups, high phagosome content and CD68 upregulation. Interactions between microglia and motoneurons changed with time after axotomy. Microglia first extend processes that end in phagocytic cups at the motoneuron surface, then they closely attach to the motoneuron while extending filopodia over the cell body. Confocal 3D analyses revealed increased microglia coverage of the motoneuron cell body surface with time after injury and the presence of CD68 granules in microglia surfaces opposed to motoneurons. Some microglia formed macroclusters associated with dying motoneurons. Microglia in these clusters display the highest CD68 expression and associate with cytotoxic T-cells. These observations are discussed in relation to current theories on microglia function around axotomized motoneurons.
New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in the Amalda I cave (Gipuzkoa, Spain)
Authors: Sánchez-Romero Laura , Benito-Calvo Alfonso , Marín-Arroyo Ana B. , Agudo-Pérez Lucía , Karampaglidis Theodoros , Rios-Garaizar Joseba 
Published: May 2020

AbstractThe Level VII of Amalda I cave (Gipuzkoa, Spain) represents one of the latest Middle Palaeolithic occupations in the Cantabrian Region. It is characterized by the presence of Middle Palaeolithic lithic industry and animal remains, with clear evidences of anthropic and carnivore manipulation. At this site, the Neanderthal presence has been questioned in relation to the role of carnivores in the accumulation of large, medium-sized and small mammals. It has also been proposed that the Neanderthal occupation could have consisted of short-term occupations, where different activities took place in a structured space within the cave. However, all hypotheses lacked any integrative analysis of the site formation processes. With the aim of understanding these processes, a combination of spatial techniques, based on GIS and inferential statistics (density analysis, hotspots tools and palaeotopographic reconstruction), along with the taphonomic study of identifiable and non-identifiable macromammals remains, were employed. This study has revealed distinct use of the cave space by Neanderthals and carnivores. The major concentrations of lithics and medium-size mammal remains were clearly accumulated by humans at the cave entrance, while the small-size mammals were gathered by carnivores in an inner zone. The activities of the Neanderthals seem to be distinctly structured, suggesting a parallel exploitation of resources.
Observation of elliptically polarized light from total internal reflection in bubbles
Authors: Miller Sawyer , Ding Yitian , Jiang Linan , Tu Xingzhou , Pau Stanley 
Published: May 2020

AbstractBubbles are ubiquitous in the natural environment, where different substances and phases of the same substance forms globules due to differences in pressure and surface tension. Total internal reflection occurs at the interface of a bubble, where light travels from the higher refractive index material outside a bubble to the lower index material inside a bubble at appropriate angles of incidence, which can lead to a phase shift in the reflected light. Linearly polarized skylight can be converted to elliptically polarized light with efficiency up to 53% by single scattering from the water-air interface. Total internal reflection from air bubble in water is one of the few sources of elliptical polarization in the natural world. Stationary and dynamic scenes of air bubbles in water in both indoor and outdoor settings are studied using an imaging polarimeter. Our results are important for studies in fluid dynamics, remote sensing, and polarimetry.
Structural dynamic studies on identification of EGCG analogues for the inhibition of Human Papillomavirus E7
Authors: Aarthy Murali , Panwar Umesh , Singh Sanjeev Kumar 
Published: May 2020

AbstractHigh risk human papillomaviruses are highly associated with the cervical carcinoma and the other genital tumors. Development of cervical cancer passes through the multistep process initiated from benign cyst to increasingly severe premalignant dysplastic lesions in an epithelium. Replication of this virus occurs in the fatal differentiating epithelium and involves in the activation of cellular DNA replication proteins. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers constrains the cells into S-phase constructing an environment favorable for genome replication and cell proliferation. To date, no suitable drug molecules exist to treat HPV infection whereas anticipation of novel anti-HPV chemotherapies with distinctive mode of actions and identification of potential drugs are crucial to a greater extent. Hence, our present study focused on identification of compounds analogue to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems towards treatment of cancer. A three dimensional similarity search on the small molecule library from natural product database using EGCG identified 11 potential small molecules based on their structural similarity. The docking strategies were implemented with acquired small molecules and identification of the key interactions between protein and compounds were carried out through binding free energy calculations. The conformational changes between the apoprotein and complexes were analyzed through simulation performed thrice demonstrating the dynamical and structural effects of the protein induced by the compounds signifying the domination. The analysis of the conformational stability provoked us to describe the features of the best identified small molecules through electronic structure calculations. Overall, our study provides the basis for structural insights of the identified potential identified small molecules and EGCG. Hence, the identified analogue of EGCG can be potent inhibitors against the HPV 16 E7 oncoprotein.
Nanoparticle delivery of a pH-sensitive prodrug of doxorubicin and a mitochondrial targeting VES-H8R8 synergistically kill multi-drug resistant breast cancer cells
Authors: Czupiel Petro , Delplace Vianney , Shoichet Molly 
Published: May 2020

AbstractMulti-drug resistance (MDR) remains a major obstacle in cancer treatment while being heavily dependent on mitochondrial activity and drug efflux. We previously demonstrated that cationic lipids, such as the vitamin E succinate modified octahistidine-octaarginine (VES-H8R8) conjugate, target mitochondria, resulting in depolarized mitochondria and inhibited drug efflux in MDR breast cancer cells. We hypothesized that the effective cell uptake, efflux inhibition, and mitochondrial depolarization properties of VES-H8R8 would synergistically enhance the toxicity of a pH-sensitive prodrug of doxorubicin (pDox) when co-encapsulated in nanoparticles (NPs). pDox was successfully synthesized and validated for pH-sensitive release from NPs under lysosome-mimicking, acidic conditions. The synergistic effect of VES-H8R8 and pDox was confirmed against MDR breast cancer cells in vitro. Importantly, synergism was only observed when VES-H8R8 and pDox were co-encapsulated in a single nanoparticulate system. The synergistic mechanism was investigated, confirming superior pDox uptake and retention, Pgp efflux inhibition, mitochondrial depolarization, and enhanced induction of ROS, and apoptosis. This work demonstrates the translational potential of doubly-loaded NPs co-encapsulating pDox with VES-H8R8 to synergistically kill MDR breast cancer cells.
Instrumentation for quantitative analysis of volatile compounds emission at elevated temperatures. Part 1: Design and implementation
Authors: Lourenço Célia , Bergin Sarah , Hodgkinson Jane , Francis Daniel , Staines Stephen E. , Saffell John R. , Walton Christopher , Tatam Ralph P. 
Published: May 2020

AbstractA novel suite of instrumentation for the characterisation of materials held inside an air-tight tube furnace operated up to 250 °C has been developed. Real-time detection of released gases (volatile organic compounds (VOCs), CO2, NO, NO2, SO2, CO and O2) was achieved combining commercial off-the-shelf (COTS) gas sensors and sorbent tubes for further qualitative and semi-quantitative analysis by gas chromatography-mass spectrometry coupled to thermal desorption (TD-GC-MS). The test system was designed to provide a controlled flow (1000 cm3 min−1) of hydrocarbon free air through the furnace. The furnace temperature ramp was set at a rate of 5 °C min−1 with 10 min dwell points at 70 °C, 150 °C, 200 °C and 250 °C to allow time for stabilisation and further headspace sampling onto sorbent tubes. Experimental design of the instrumentation is described here and an example data set upon exposure to a gas sample is presented.
Opposite Roles of the JMJD1A Interaction Partners MDFI and MDFIC in Colorectal Cancer
Authors: Sui Yuan , Li Xiaomeng , Oh Sangphil , Zhang Bin , Freeman Willard M. , Shin Sook , Janknecht Ralf 
Published: May 2020

AbstractMyoD family inhibitor (MDFI) and MDFI domain-containing (MDFIC) are homologous proteins known to regulate myogenic transcription factors. Hitherto, their role in cancer is unknown. We discovered that MDFI is up- and MDFIC downregulated in colorectal tumors. Mirroring these different expression patterns, MDFI stimulated and MDFIC inhibited growth of HCT116 colorectal cancer cells. Further, MDFI and MDFIC interacted with Jumonji C domain-containing (JMJD) 1 A, a histone demethylase and epigenetic regulator involved in colorectal cancer. JMJD1A influenced transcription of several genes that were also regulated by MDFI or MDFIC. Notably, the HIC1 tumor suppressor gene was stimulated by JMJD1A and MDFIC, but not by MDFI, and HIC1 overexpression phenocopied the growth suppressive effects of MDFIC in HCT116 cells. Similar to colorectal cancer, MDFI was up- and MDFIC downregulated in breast, ovarian and prostate cancer, but both were overexpressed in brain, gastric and pancreatic tumors that implies MDFIC to also promote tumorigenesis in certain tissues. Altogether, our data suggest a tumor modulating function for MDFI and MDFIC in colorectal and other cancers that may involve their interaction with JMJD1A and a MDFIC→HIC1 axis.
Epithelial-interleukin-1 inhibits collagen formation by airway fibroblasts: Implications for asthma
Authors: Osei Emmanuel T. , B. Mostaço-Guidolin Leila , Hsieh Aileen , Warner Stephanie M. , AL-Fouadi May , Wang Mary , Cole Darren J. , Maksym Geoffrey N. , S. Hallstrand Teal , Timens Wim , Brandsma Corry-Anke , Heijink Irene H. , Hackett Tillie-Louise. 
Published: May 2020

AbstractIn asthma, the airway epithelium has an impaired capacity to differentiate and plays a key role in the development of airway inflammation and remodeling through mediator release. The study objective was to investigate the release of (IL)-1 family members from primary airway epithelial-cells during differentiation, and how they affect primary airway fibroblast (PAF)-induced inflammation, extracellular matrix (ECM) production, and collagen I remodeling. The release of IL-1α/β and IL-33 during airway epithelial differentiation was assessed over 20-days using air-liquid interface cultures. The effect of IL-1 family cytokines on airway fibroblasts grown on collagen-coated well-plates and 3-dimensional collagen gels was assessed by measurement of inflammatory mediators and ECM proteins by ELISA and western blot, as well as collagen fiber formation using non-linear optical microscopy after 24-hours. The production of IL-1α is elevated in undifferentiated asthmatic-PAECs compared to controls. IL-1α/β induced fibroblast pro-inflammatory responses (CXCL8/IL-8, IL-6, TSLP, GM-CSF) and suppressed ECM-production (collagen, fibronectin, periostin) and the cell’s ability to repair and remodel fibrillar collagen I via LOX, LOXL1 and LOXL2 activity, as confirmed by inhibition with β-aminopropionitrile. These data support a role for epithelial-derived-IL-1 in the dysregulated repair of the asthmatic-EMTU and provides new insights into the contribution of airway fibroblasts in inflammation and airway remodeling in asthma.
New capabilities of Sentinel-2A/B satellites combined with in situ data for monitoring small harmful algal blooms in complex coastal waters
Authors: Caballero Isabel , Fernández Raúl , Escalante Oscar Moreno , Mamán Luz , Navarro Gabriel 
Published: May 2020

AbstractThe increased frequency of harmful algal blooms (HABs) is a major environmental concern worldwide, resulting not only in increased treatment costs for drinking water but also in impacts on tourism, commercial fishing and aquaculture and risks to human and animal health. Traditional strategies with ship-based approaches based on field sampling and laboratory analysis have been adopted to assess HABs. However, these methods are labour intensive and costly and do not provide synoptic views of the bloom conditions. Here, we show that the Sentinel-2 twin satellite mission of the Copernicus programme, in combination with in situ data, is a powerful tool that can offer valuable spatiotemporal information about a bloom of the dinoflagellate Lingulodinium polyedra that occurred on the SW Iberian Peninsula. Using the robust ACOLITE atmospheric correction processor combined with the normalized difference chlorophyll index (NDCI), the enhanced mapping of small blooms can be performed at a 10 m spatial resolution, revealing surface patches and a heterogeneous distribution. This research also demonstrates the improved capabilities of Sentinel-2 compared to those of Landsat-8 and Sentinel-3 for continuous monitoring. The Sentinel-3 and Sentinel-2 missions provide ecosystem observations that allow the environmental community and water managers to evaluate changes in water quality and bloom distribution and that facilitate field-based measurements. Therefore, the value added by the Copernicus products in terms of frequency and synoptic observations is of paramount importance for ecological and management purposes at regional and national scales.
Ovarian Cancer Exosomes Trigger Differential Biophysical Response in Tumor-Derived Fibroblasts
Authors: Lee Amy H. , Ghosh Deepraj , Quach Nhat , Schroeder Devin , Dawson Michelle R. 
Published: May 2020

AbstractExosomes are cell-secreted microvesicles that play important roles in epithelial ovarian cancer (EOC) progression, as they are constantly secreted into ascites fluids. While cells spontaneously release exosomes, alterations in intracellular calcium or extracellular pH can release additional exosomes. Yet, little is known about how these exosomes compare to those that are continuously released without stimulation and how they mediate cellular activities important in cancer progression. Here, we demonstrate that chelation of extracellular calcium leads to release of chelation-induced exosomes (CI-exosomes) from OVCAR-3 EOC cells. CI-exosomes display a unique miRNA profile compared to naturally secreted exosomes (SEC-exosomes). Furthermore, treatment with CI- and SEC-exosomes leads to differential biophysical and functional changes including, adhesion and migration in EOC-derived fibroblasts that suggest the development of a malignant tumor microenvironment. This result highlights how tumor environmental factors contribute to heterogeneity in exosome populations and how different exosome populations mediate diversity in stromal cell behavior.
Health status among greenhouse workers exposed to different levels of pesticides: A genetic matching analysis
Authors: Xie Yongxin , Li Jiangping , Guo Xin , Zhao Ji , Yang Biao , Xiao Wenwen , Yang Huifang 
Published: May 2020

Abstract(1) Objective: Greenhouse workers are considered a special occupational group who are exposed to more toxic and harmful substances than ordinary farmers. The health problem of this group is a public health problem that warrants attention. Taking greenhouse workers in Ningxia, China, as the research sample, this study analyzed the health risk to practitioners posed by the greenhouse working environment. (2) Method: To analyze the relationship between pesticide exposure and the health of greenhouse workers, the genetic matching method was used to exclude the influence of covariates on the results. (3) Results: The results showed a statistical significance regarding the prevalence of cardiovascular diseases (CVD), skeletal muscle system diseases (SMSD) and digestive diseases between the different exposure groups. Researching the disease symptoms found that different levels of exposure to pesticides in greenhouses could cause multisystem and multisymptom discomfort. In addition to some irritant symptoms such as eye itching, itching, and sneezing, there were also differences in terms of the frequency of discomfort such as back pain, a decline in sleep quality, memory loss, joint pain, swelling and weakness, upper abdominal pain and flatulence, in the different exposure groups. (4) Conclusion: Different levels of exposure to pesticides in greenhouses may be one of the risk factors for practitioners to suffer from various systemic diseases, affecting their health and work efficiency. This hazard is manifested not only in some acute irritant symptoms but also in chronic diseases due to long-term exposure.
Cave bacteria-induced amorphous calcium carbonate formation
Authors: Enyedi Nóra Tünde , Makk Judit , Kótai László , Berényi Bernadett , Klébert Szilvia , Sebestyén Zoltán , Molnár Zsombor , Borsodi Andrea K. , Leél-Őssy Szabolcs , Demény Attila , Németh Péter 
Published: May 2020

AbstractAmorphous calcium carbonate (ACC) is a precursor of crystalline calcium carbonates that plays a key role in biomineralization and polymorph evolution. Here, we show that several bacterial strains isolated from a Hungarian cave produce ACC and their extracellular polymeric substance (EPS) shields ACC from crystallization. The findings demonstrate that bacteria-produced ACC forms in water-rich environment at room temperature and is stable for at least half year, which is in contrast to laboratory-produced ACC that needs to be stored in a desiccator and kept below 10 °C for avoiding crystallization. The ACC-shielding EPS consists of lipids, proteins, carbohydrates and nucleic acids. In particular, we identified large amount of long-chain fatty acid components. We suggest that ACC could be enclosed in a micella-like formula within the EPS that inhibits water infiltration. As the bacterial cells lyse, the covering protective layer disintegrates, water penetrates and the unprotected ACC grains crystallize to calcite. Our study indicates that bacteria are capable of producing ACC, and we estimate its quantity in comparison to calcite presumably varies up to 20% depending on the age of the colony. Since diverse bacterial communities colonize the surface of cave sediments in temperate zone, we presume that ACC is common in these caves and its occurrence is directly linked to bacterial activity and influences the geochemical signals recorded in speleothems.