bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early exposure to antibiotic drugs and risk for psychiatric disorders: a population-based study
Authors: Lavebratt Catharina , Yang Liu L. , Giacobini MaiBritt , Forsell Yvonne , Schalling Martin , Partonen Timo , Gissler Mika 
Published: November 2019

AbstractEarly life exposure to infection, anti-infectives and altered immune activity have been associated with elevated risk of some psychiatric disorders. However, the risk from exposure in fetal life has been proposed to be confounded by familial factors. The hypothesis of this study is that antibiotic drug exposure during the fetal period and the first two postnatal years is associated with risk for later development of psychiatric disorders in children. All births in Finland between 1996 and 2012, 1 million births, were studied for antibiotic drug exposure: mothers during pregnancy and the children the first two postnatal years. The children were followed up for a wide spectrum of psychiatric diagnoses and psychotropic drug treatment until 2014. Cox proportional hazards modeling was used to estimate effects of antibiotic drug exposure on offspring psychiatric disorders. Modestly (10–50%) increased risks were found on later childhood development of sleep disorders, ADHD, conduct disorder, mood and anxiety disorders, and other behavioral and emotional disorders with childhood onset (ICD-10 F98), supported by increased risks also for childhood psychotropic medication. The prenatal exposure effects detected were not explained by explored familial confounding, nor by registered maternal infections. To conclude, this longitudinal nation-wide study shows that early life antibiotic drug exposure is associated with an increased risk for childhood development of psychopathology. Given the high occurrence of early-life antibiotic exposure, these findings are of public health relevance. Whether the associations reflect effects of the antibiotic drug use or of the targeted infections remains to be explored further.
DAPK1 loss triggers tumor invasion in colorectal tumor cells
Authors: Steinmann Sara , Kunze Philipp , Hampel Chuanpit , Eckstein Markus , Bertram Bramsen Jesper , Muenzner Julienne K. , Carlé Birgitta , Ndreshkjana Benardina , Kemenes Stephan , Gasparini Pierluigi , Friedrich Oliver , Andersen Claus , Geppert Carol , Wang Shengbao , Eyupoglu Ilker , Bäuerle Tobias , Hartmann Arndt , Schneider-Stock Regine 
Published: November 2019

AbstractColorectal cancer (CRC) is one of the leading cancer-related causes of death worldwide. Despite the improvement of surgical and chemotherapeutic treatments, as of yet, the disease has not been overcome due to metastasis to distant organs. Hence, it is of great relevance to understand the mechanisms responsible for metastasis initiation and progression and to identify novel metastatic markers for a higher chance of preventing the metastatic disease. The Death-associated protein kinase 1 (DAPK1), recently, has been shown to be a potential candidate for regulating metastasis in CRC. Hence, the aim of the study was to investigate the impact of DAPK1 protein on CRC aggressiveness. Using CRISPR/Cas9 technology, we generated DAPK1-deficient HCT116 monoclonal cell lines and characterized their knockout phenotype in vitro and in vivo. We show that loss of DAPK1 implemented changes in growth pattern and enhanced tumor budding in vivo in the chorioallantoic membrane (CAM) model. Further, we observed more tumor cell dissemination into chicken embryo organs and increased invasion capacity using rat brain 3D in vitro model. The novel identified DAPK1-loss gene expression signature showed a stroma typical pattern and was associated with a gained ability for remodeling the extracellular matrix. Finally, we suggest the DAPK1-ERK1 signaling axis being involved in metastatic progression of CRC. Our results highlight DAPK1 as an anti-metastatic player in CRC and suggest DAPK1 as a potential predictive biomarker for this cancer type.
NF-κB2 signalling in enteroids modulates enterocyte responses to secreted factors from bone marrow-derived dendritic cells
Authors: Jones Lauren G. , Vaida Andra , Thompson Louise M. , Ikuomola Felix I. , Caamaño Jorge H. , Burkitt Michael D. , Miyajima Fabio , Williams Jonathan M. , Campbell Barry J. , Pritchard D. Mark , Duckworth Carrie A. 
Published: November 2019

AbstractAlternative pathway NF-κB signalling regulates susceptibility towards developing inflammatory bowel disease (IBD), colitis-associated cancer and sepsis-associated intestinal epithelial cell apoptosis and shedding. However, the cell populations responsible for the perturbed alternative pathway NF-κB signalling in intestinal mucosal pathology remain unclear. In order to investigate the contribution of the epithelial compartment, we have tested whether NF-κB2 regulated transcription in intestinal epithelial cells controls the intestinal epithelial response to cytokines that are known to disrupt intestinal barrier permeability. Enteroids were generated from the proximal, middle and distal regions of small intestine (SI) from C57BL/6J wild-type mice and displayed region-specific morphology that was maintained during sub-culture. Enteroids treated with 100 ng/mL TNF were compared with corresponding regions of SI from C57BL/6J mice treated systemically with 0.33 mg/kg TNF for 1.5 h. TNF-induced apoptosis in all regions of the intestine in vitro and in vivo but resulted in Paneth cell degranulation only in proximal tissue-derived SI and enteroids. TNF also resulted in increased enteroid sphericity (quantified as circularity from two-dimensional bright field images). This response was dose and time-dependent and correlated with active caspase-3 immunopositivity. Proximal tissue-derived enteroids generated from Nfκb2−/− mice showed a significantly blunted circularity response following the addition of TNF, IFNγ, lipopolysaccharide (LPS) activated C57BL/6J-derived bone marrow-derived dendritic cells (BMDC) and secreted factors from LPS-activated BMDCs. However, Nfκb1−/− mouse-derived enteroids showed no significant changes in response to these stimuli. In conclusion, the selection of SI region is important when designing enteroid studies as region-specific identity and response to stimuli such as TNF are maintained in culture. Intestinal epithelial cells are at least partially responsible for regulating their own fate by modulating NF-κB2 signalling in response to stimuli known to be involved in multiple intestinal and systemic diseases. Future studies are warranted to investigate the therapeutic potential of intestinal epithelial NF-κB2 inhibition.
Learning dynamical information from static protein and sequencing data
Authors: Pearce Philip , Woodhouse Francis G. , Forrow Aden , Kelly Ashley , Kusumaatmaja Halim , Dunkel Jörn 
Published: November 2019

AbstractMany complex processes, from protein folding to neuronal network dynamics, can be described as stochastic exploration of a high-dimensional energy landscape. Although efficient algorithms for cluster detection in high-dimensional spaces have been developed over the last two decades, considerably less is known about the reliable inference of state transition dynamics in such settings. Here we introduce a flexible and robust numerical framework to infer Markovian transition networks directly from time-independent data sampled from stationary equilibrium distributions. We demonstrate the practical potential of the inference scheme by reconstructing the network dynamics for several protein-folding transitions, gene-regulatory network motifs, and HIV evolution pathways. The predicted network topologies and relative transition time scales agree well with direct estimates from time-dependent molecular dynamics data, stochastic simulations, and phylogenetic trees, respectively. Owing to its generic structure, the framework introduced here will be applicable to high-throughput RNA and protein-sequencing datasets, and future cryo-electron microscopy (cryo-EM) data.
Crystal structure and receptor-interacting residues of MYDGF — a protein mediating ischemic tissue repair
Authors: Ebenhoch Rebecca , Akhdar Abbas , Reboll Marc R. , Korf-Klingebiel Mortimer , Gupta Priyanka , Armstrong Julie , Huang Yining , Frego Lee , Rybina Irina , Miglietta John , Pekcec Anton , Wollert Kai C. , Nar Herbert 
Published: November 2019

AbstractMyeloid-derived growth factor (MYDGF) is a paracrine-acting protein that is produced by bone marrow-derived monocytes and macrophages to protect and repair the heart after myocardial infarction (MI). This effect can be used for the development of protein-based therapies for ischemic tissue repair, also beyond the sole application in heart tissue. Here, we report the X-ray structure of MYDGF and identify its functionally relevant receptor binding epitope. MYDGF consists of a 10-stranded β-sandwich with a folding topology showing no similarities to other cytokines or growth factors. By characterizing the epitope of a neutralizing antibody and utilizing functional assays to study the activity of surface patch-mutations, we were able to localize the receptor interaction interface to a region around two surface tyrosine residues 71 and 73 and an adjacent prominent loop structure of residues 97–101. These findings enable structure-guided protein engineering to develop modified MYDGF variants with potentially improved properties for clinical use.
Decoupling of mechanical properties and ionic conductivity in supramolecular lithium ion conductors
Authors: Mackanic David G. , Yan Xuzhou , Zhang Qiuhong , Matsuhisa Naoji , Yu Zhiao , Jiang Yuanwen , Manika Tuheen , Lopez Jeffrey , Yan Hongping , Liu Kai , Chen Xiaodong , Cui Yi , Bao Zhenan 
Published: November 2019

AbstractThe emergence of wearable electronics puts batteries closer to the human skin, exacerbating the need for battery materials that are robust, highly ionically conductive, and stretchable. Herein, we introduce a supramolecular design as an effective strategy to overcome the canonical tradeoff between mechanical robustness and ionic conductivity in polymer electrolytes. The supramolecular lithium ion conductor utilizes orthogonally functional H-bonding domains and ion-conducting domains to create a polymer electrolyte with unprecedented toughness (29.3 MJ m−3) and high ionic conductivity (1.2 × 10−4 S cm−1 at 25 °C). Implementation of the supramolecular ion conductor as a binder material allows for the creation of stretchable lithium-ion battery electrodes with strain capability of over 900% via a conventional slurry process. The supramolecular nature of these battery components enables intimate bonding at the electrode-electrolyte interface. Combination of these stretchable components leads to a stretchable battery with a capacity of 1.1 mAh cm−2 that functions even when stretched to 70% strain. The method reported here of decoupling ionic conductivity from mechanical properties opens a promising route to create high-toughness ion transport materials for energy storage applications.
Magnetocaloric materials with ultra-small magnetic nanoparticles working at room temperature
Authors: Dudek M. R. , Dudek K. K. , Wolak W. , Wojciechowski K. W. , Grima J. N. 
Published: November 2019

AbstractThrough the use of the Monte Carlo simulations utilising the mean-field approach, we show that a dense assembly of separated ultra-small magnetic nanoparticles embedded into a non-magnetic deformable matrix can be characterized by a large isothermal magnetic entropy change even upon applying a weak magnetic field with values much smaller than one Tesla. We also show that such entropy change may be very significant in the vicinity of the room temperature which effect normally requires an application of a strong external magnetic field. The deformable matrix chosen in this work as a host for magnetic nanoparticles adopts a thin film form with a large surface area to volume ratio. This in turn in combination with a strong magneto-volume coupling exhibited by this material allows us to show its suitability to be used in the case of a variety of applications utilising local cooling/heating such as future magnetic refrigerants.
Revealing universal quantum contextuality through communication games
Authors: Pan A. K. 
Published: November 2019

AbstractAn ontological model of an operational theory is considered to be universally noncontextual if both preparation and measurement noncontextuality assumptions are satisfied in that model. In this report, we first generalize the logical proofs of quantum preparation and measurement contextuality for qubit system for any odd number of preparations and measurements. Based on the logical proof, we derive testable universally non-contextual inequalities violated by quantum theory. We then propose a class of two-party communication games and show that the average success probability of winning such games is solely linked to suitable Bell expression whose local bound is greater than universal non-contextual bound. Thus, for a given state, even if quantum theory does not exhibit non-locality, it may still reveal non-classicality by violating the universal non-contextual bound. Further, we consider a different communication game to demonstrate that for a given choices of observables in quantum theory, even if there is no logical proof of preparation and measurement contextuality exist, the universal quantum contextuality can be revealed through that communication game. Such a game thus test a weaker form of universal non-contextuality with minimal assumption.
Comparing methods for comparing networks
Authors: Tantardini Mattia , Ieva Francesca , Tajoli Lucia , Piccardi Carlo 
Published: November 2019

AbstractWith the impressive growth of available data and the flexibility of network modelling, the problem of devising effective quantitative methods for the comparison of networks arises. Plenty of such methods have been designed to accomplish this task: most of them deal with undirected and unweighted networks only, but a few are capable of handling directed and/or weighted networks too, thus properly exploiting richer information. In this work, we contribute to the effort of comparing the different methods for comparing networks and providing a guide for the selection of an appropriate one. First, we review and classify a collection of network comparison methods, highlighting the criteria they are based on and their advantages and drawbacks. The set includes methods requiring known node-correspondence, such as DeltaCon and Cut Distance, as well as methods not requiring a priori known node-correspondence, such as alignment-based, graphlet-based, and spectral methods, and the recently proposed Portrait Divergence and NetLSD. We test the above methods on synthetic networks and we assess their usability and the meaningfulness of the results they provide. Finally, we apply the methods to two real-world datasets, the European Air Transportation Network and the FAO Trade Network, in order to discuss the results that can be drawn from this type of analysis.
Quantification of the morphological characteristics of hESC colonies
Authors: Orozco-Fuentes Sirio , Neganova Irina , Wadkin Laura E. , Baggaley Andrew W. , Barrio Rafael A. , Lako Majlinda , Shukurov Anvar , Parker Nicholas G. 
Published: November 2019

AbstractThe maintenance of the undifferentiated state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1–1.1 $${{\bf{\text{mm}}}}^{{\bf{2}}}$$mm2) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area $${\boldsymbol{A}}$$A. Large colonies (A > 0.6 mm2) have cells with smaller nuclei and a short intercellular distance when compared with small colonies (A < 0.2 mm2). The gaps between the cells, which are present in small and medium sized colonies with A ≤ 0.6 mm2, disappear in large colonies (A > 0.6 mm2) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database.
Combined organic biomarker and use-wear analyses of stone artefacts from Liang Bua, Flores, Indonesia
Authors: Luong Susan , Tocheri Matthew W. , Hayes Elspeth , Sutikna Thomas , Fullagar Richard , Saptomo E. Wahyu , Jatmiko  , Roberts Richard G. 
Published: November 2019

AbstractOrganic biomarker and lithic use-wear analyses of archaeological implements manufactured and/or used by hominins in the past offers a means of assessing how prehistoric peoples utilised natural resources. Currently, most studies focus on one of these techniques, rather than using both in sequence. This study aims to assess the potential of combining both methods to analyse stone artefacts, using a set of 69 stones excavated from the cave site of Liang Bua (Flores, Indonesia). Prior to chemical analysis, an initial inspection of the artefacts revealed potential use-wear traces but no visible residues. Gas chromatography mass spectrometry (GC-MS) analysis, including the targeting of 86 lipids, terpenes, terpenoids, alkanes and their analogues, found compounds with plant or animal origin on 27 of the 69 stones. The artefacts were subsequently cleaned, and use-wear analysis identified traces of use on 43 artefacts. Use-wear analysis confirmed traces of use on 23 of the 27 artefacts with potential use-residues that were determined by GC-MS. The GC-MS results were broadly consistent with the functional classes identified in the later use-wear analysis. This inclusive approach for stone artefact analysis strengthens the identifications made through multiple lines of enquiry. There remain conflicts and uncertainties in specific cases, suggesting the need for further refinement and analyses of the relationships between use-wear and residues.
Influence of Vegetation Coverage and Climate Environment on Soil Organic Carbon in the Qilian Mountains
Authors: Wan Qiaozhuo , Zhu Guofeng , Guo Huiwen , Zhang Yu , Pan Hanxiong , Yong Leilei , Ma Huiying 
Published: November 2019

AbstractStudying the spatial distribution pattern of soil organic carbon and its influencing factors is essential for understanding the carbon cycle in terrestrial ecosystems. Soil samples from four active layers of typical vegetation types (Populus, subalpine shrubs, Picea crassifolia Kom, and alpine meadow) in the upper reaches of Shiyang River basin in the Qilian Mountains were collected to determine the soil organic carbon content and physicochemical properties. The results show the following: (1) There are significant differences in the vertical distribution of Soil organic carbon in the watershed, and the Soil organic carbon content decreases significantly with increasing soil depth. (2) Mainly affected by biomass, the organic carbon content of different vegetation types in different soil layers is as follows: Alpine meadow > Picea crassifolia Kom > Populus > Subalpine shrub, and the soil organic carbon content increases with increasing altitude. Under different vegetation types, the Soil organic content is the highest in the 0–30 cm soil profile, and the maximum value often appears in the 0–10 cm layer, then gradually decreases downward. (3) When soil organic carbon is determined in different vegetation types in the study area, the change of hydrothermal factors has little effect on soil organic carbon content in the short term.
Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Authors: Everaert Celine , Helsmoortel Hetty , Decock Anneleen , Hulstaert Eva , Van Paemel Ruben , Verniers Kimberly , Nuytens Justine , Anckaert Jasper , Nijs Nele , Tulkens Joeri , Dhondt Bert , Hendrix An , Mestdagh Pieter , Vandesompele Jo 
Published: November 2019

AbstractRNA profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. However, despite enormous interest in extracellular nucleic acids, RNA sequencing methods to quantify the total RNA content outside cells are rare. Here, we evaluate the performance of the SMARTer Stranded Total RNA-Seq method in human platelet-rich plasma, platelet-free plasma, urine, conditioned medium, and extracellular vesicles (EVs) from these biofluids. We found the method to be accurate, precise, compatible with low-input volumes and able to quantify a few thousand genes. We picked up distinct classes of RNA molecules, including mRNA, lncRNA, circRNA, miscRNA and pseudogenes. Notably, the read distribution and gene content drastically differ among biofluids. In conclusion, we are the first to show that the SMARTer method can be used for unbiased unraveling of the complete transcriptome of a wide range of biofluids and their extracellular vesicles.
Secondary formation damage of low-pressure layer during commingled production in multilayered tight gas reservoirs
Authors: Ding Jingchen , Yan Changhui , He Yongming , Wang Changcheng 
Published: November 2019

AbstractThis paper experimentally investigates fluid back-flow behavior and formation damage during commingled production in multilayered tight gas reservoirs. The development of fluid back-flow in commingled tight gas reservoirs was simulated using a newly designed experimental platform. The results indicate that when there is a pressure difference between different layers during commingled production from tight gas reservoir, water produced from the high-pressure layer will invade the low-pressure layer along with gas back-flow and will accumulate in the near-wellbore area. This will lead to an increase in water saturation and a decline in permeability in the low-pressure layer and result in a significant reduction in ultimate recovery. The outcomes of these experiments demonstrate that as well as the formation damage caused by the working fluid during drilling and fracturing, “Secondary Formation Damage” also occurs during commingled production in multilayered tight gas reservoirs. This secondary formation damage mainly occurs in the near-wellbore area of low-pressure layers and is more severe with greater proximity to the wellbore. Through further experimentation to assess the factors influencing secondary formation damage, it is shown that the degree of secondary formation damage increases with decreasing original formation pressure, original water saturation, and permeability in the lower-pressure layer.