bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature
Authors: Gendoo Deena M. A. , Zon Michael , Sandhu Vandana , Manem Venkata S. K. , Ratanasirigulchai Natchar , Chen Gregory M. , Waldron Levi , Haibe-Kains Benjamin 
Published: June 2019

AbstractA wealth of transcriptomic and clinical data on solid tumours are under-utilized due to unharmonized data storage and format. We have developed the MetaGxData package compendium, which includes manually-curated and standardized clinical, pathological, survival, and treatment metadata across breast, ovarian, and pancreatic cancer data. MetaGxData is the largest compendium of curated transcriptomic data for these cancer types to date, spanning 86 datasets and encompassing 15,249 samples. Open access to standardized metadata across cancer types promotes use of their transcriptomic and clinical data in a variety of cross-tumour analyses, including identification of common biomarkers, and assessing the validity of prognostic signatures. Here, we demonstrate that MetaGxData is a flexible framework that facilitates meta-analyses by using it to identify common prognostic genes in ovarian and breast cancer. Furthermore, we use the data compendium to create the first gene signature that is prognostic in a meta-analysis across 3 cancer types. These findings demonstrate the potential of MetaGxData to serve as an important resource in oncology research, and provide a foundation for future development of cancer-specific compendia.
Reconstruction of bovine spermatozoa substances distribution and morphological differences between Holstein and Korean native cattle using three-dimensional refractive index tomography
Authors: Jiang Hao , Kwon Jeong-woo , Lee Sumin , Jo Yu-Jin , Namgoong Suk , Yao Xue-rui , Yuan Bao , Zhang Jia-bao , Park Yong-Keun , Kim Nam-Hyung 
Published: June 2019

AbstractMeasurements of the three-dimensional (3D) structure of spermatozoon are crucial for the study of developmental biology and for the evaluation of in vitro fertilization. Here, we present 3D label-free imaging of individual spermatozoon and perform quantitative analysis of bovine, porcine, and mouse spermatozoa morphologies using refractive index tomography. Various morphological and biophysical properties were determined, including the internal structure, volume, surface area, concentration, and dry matter mass of individual spermatozoon. Furthermore, Holstein cows and Korean native cattle spermatozoa were systematically analyzed and revealed significant differences in spermatozoa head length, head width, midpiece length, and tail length between the two breeds. This label-free imaging approach provides a new technique for understanding the physiology of spermatozoa.
The quantum thermodynamic force responsible for quantum state transformation and the flow and backflow of information
Authors: Ahmadi B. , Salimi S. , Khorashad A. S. , Kheirandish F. 
Published: June 2019

AbstractWhy do quantum evolutions occur and why do they stop at certain points? In classical thermodynamics affinity was introduced to predict in which direction an irreversible process proceeds. In this paper the quantum mechanical counterpart of the classical affinity is found. It is shown that the quantum version of affinity can predict in which direction a process evolves. A new version of the second law of thermodynamics is derived through quantum affinity for energy-incoherent state interconversion under thermal operations. we will also see that the quantum affinity can be a good candidate to be responsible, as a force, for driving the flow and backflow of information in Markovian and non-Markovian evolutions. Finally we show that the rate of quantum coherence can be interpreted as the pure quantum mechanical contribution of the total thermodynamic force and flow. Thus it is seen that, from a thermodynamic point of view, any interaction from the outside with the system or any measurement on the system may be represented by a quantum affinity.
PAR-4 overcomes chemo-resistance in breast cancer cells by antagonizing cIAP1
Authors: Guo Haihong , Treude Fabian , Krämer Oliver H. , Lüscher Bernhard , Hartkamp Jörg 
Published: June 2019

AbstractMost deaths from breast cancer result from tumour recurrence, which is typically an incurable disease. Down-regulation of the pro-apoptotic tumour suppressor protein prostate apoptosis response-4 (PAR-4) is required for breast cancer recurrence and resistance to chemotherapy. Recent advances in the analysis of apoptotic signalling networks have uncovered an important role for activation of caspase-8 following DNA damage by genotoxic drugs. DNA damage induces depletion of IAP proteins and causes caspase-8 activation by promoting the formation of a cytosolic cell death complex. We demonstrate that loss of PAR-4 in triple negative breast cancer cell lines (TNBC) mediates resistance to DNA damage-induced apoptosis and prevents activation of caspase-8. Moreover, loss of PAR-4 prevents DNA damage-induced cIAP1 depletion. PAR-4 functions downstream of caspase-8 by cleavage-induced nuclear translocation of the C-terminal part and we demonstrate that nuclear translocation of the C-terminal PAR-4 fragment leads to depletion of cIAP1 and subsequent caspase-8 activation. Specifically targeting cIAP1 with RNAi or Smac mimetics (LCL161) overcomes chemo-resistance induced by loss of PAR-4 and restores caspase-8 activation. Our data identify cIAP1 as important downstream mediator of PAR-4 and we provide evidence that combining Smac mimetics and genotoxic drugs creates vulnerability for synthetic lethality in TNBC cells lacking PAR-4.
Contraction of distance and duration production in autism spectrum disorder
Authors: Honma Motoyasu , Itoi Chihiro , Midorikawa Akira , Terao Yasuo , Masaoka Yuri , Kuroda Takeshi , Futamura Akinori , Shiromaru Azusa , Ohta Haruhisa , Kato Nobumasa , Kawamura Mitsuru , Ono Kenjiro 
Published: June 2019

AbstractAutism spectrum disorder (ASD) presents certain hallmark features associated with cognitive and social functions, however, the ability to estimate self-generated distance and duration in individuals with ASD are unclear. We compared the performance of 20 ASD individuals with 20 typical developments (TDs) with respect to two tasks: (1) the drawing of a line of a specified distance (10 or 20 cm) and (2) waiting for a specified time (10 or 20 s). We observed that both the line distances and waiting times were substantially shorter in the ASD group than in the TD group. Furthermore, a trait of “attention to detail,” as measured by the Autism-Spectrum Quotient, correlated with some distance and duration productions observed in individuals with ASD. We suggest that attentional functions are related to the contraction of distance and duration in ASD.
Sniffer cells for the detection of neural Angiotensin II in vitro
Authors: Farmer George E. , Amune Anna , Bachelor Martha E. , Duong Phong , Yuan Joseph P. , Cunningham J. Thomas 
Published: June 2019

AbstractNeuropeptide release in the brain has traditionally been difficult to observe. Existing methods lack temporal and spatial resolution that is consistent with the function and size of neurons. We use cultured “sniffer cells” to improve the temporal and spatial resolution of observing neuropeptide release. Sniffer cells were created by stably transfecting Chinese Hamster Ovary (CHO) cells with plasmids encoding the rat angiotensin type 1a receptor and a genetically encoded Ca2+ sensor. Isolated, cultured sniffer cells showed dose-dependent increases in fluorescence in response to exogenously applied angiotensin II and III, but not other common neurotransmitters. Sniffer cells placed on the median preoptic nucleus (a presumptive site of angiotensin release) displayed spontaneous activity and evoked responses to either electrical or optogenetic stimulation of the subfornical organ. Stable sniffer cell lines could be a viable method for detecting neuropeptide release in vitro, while still being able to distinguish differences in neuropeptide concentration.
A Selective FGFR inhibitor AZD4547 suppresses RANKL/M-CSF/OPG-dependent ostoclastogenesis and breast cancer growth in the metastatic bone microenvironment
Authors: Kang Jinho , Choi Yoon Ji , Seo Bo Yeon , Jo Ukhyun , Park Serk In , Kim Yeul Hong , Park Kyong Hwa 
Published: June 2019

AbstractAberrant activation of fibroblast growth factor receptor (FGFR) signalling contributes to progression and metastasis of many types of cancers including breast cancer. Accordingly, FGFR targeted tyrosine kinase inhibitors (TKIs) are currently under development. However, the efficacy of FGFR TKIs in the bone microenvironment where breast cancer cells most frequently metastasize and also where FGFR is biologically active, has not been clearly investigated. We investigated the FGFR-mediated interactions among cancer and the bone microenvironment stromal cells (osteoblasts and osteoclasts), and also the effects of FGFR inhibition in bone metastasis. We showed that addition of culture supernatant from the MDA-MB-134-VI FGFR-amplified breast cancer cells-activated FGFR siganalling in osteoblasts, including increased expression of RANKL, M-CSF, and osteoprotegerin (OPG). Further in vitro analyses showed that AZD4547, an FGFR TKI currently in clinical trials for breast cancer, decreased RANKL and M-CSF, and subsequently RANKL and M-CSF-dependent osteoclastogenesis of murine bone marrow monocytes. Moreover, AZD4547 suppressed osteoclastogenesis and tumor-induced osteolysis in an orthotopic breast cancer bone metastasis mouse model using FGFR non-amplified MDA-MB-231 cells. Collectively, our results support that FGFR inhibitors inhibit the bone microenvironment stromal cells including osteoblasts and osteoclasts, and effectively suppress both tumor and stromal compartments of bone metastasis.
Substrate mediated nitridation of niobium into superconducting Nb2N thin films for phase slip study
Authors: Gajar Bikash , Yadav Sachin , Sawle Deepika , Maurya Kamlesh K. , Gupta Anurag , Aloysius R. P. , Sahoo Sangeeta 
Published: June 2019

AbstractHere we report a novel nitridation technique for transforming niobium into hexagonal Nb2N which appears to be superconducting below 1K. The nitridation is achieved by high temperature annealing of Nb films grown on Si3N4/Si (100) substrate under high vacuum. The structural characterization directs the formation of a majority Nb2N phase while the morphology shows granular nature of the films. The temperature dependent resistance measurements reveal a wide metal-to-superconductor transition featuring two distinct transition regions. The region close to the normal state varies strongly with the film thickness, whereas, the second region in the vicinity of the superconducting state remains almost unaltered but exhibiting resistive tailing. The current-voltage characteristics also display wide transition embedded with intermediate resistive states originated by phase slip lines. The transition width in current and the number of resistive steps depend on film thickness and they both increase with decrease in thickness. The broadening in transition width is explained by progressive establishment of superconductivity through proximity coupled superconducting nano-grains while finite size effects and quantum fluctuation may lead to the resistive tailing. Finally, by comparing with Nb control samples, we emphasize that Nb2N offers unconventional superconductivity with promises in the field of phase slip based device applications.
Propionic Acid Induces Gliosis and Neuro-inflammation through Modulation of PTEN/AKT Pathway in Autism Spectrum Disorder
Authors: Abdelli Latifa S. , Samsam Aseela , Naser Saleh A. 
Published: June 2019

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by glia over-proliferation, neuro-inflammation, perturbed neural circuitry, and gastrointestinal symptoms. The role of gut dys-biosis in ASD is intriguing and should be elucidated. We investigated the effect of Propionic acid (PPA), a short-chain fatty acid (SCFA) and a product of dys-biotic ASD gut, on human neural stem cells (hNSCs) proliferation, differentiation and inflammation. hNSCs proliferated to 66 neuropsheres when exposed to PPA versus 45 in control. The neurosphere diameter also increased at day 10 post PPA treatment to (Mean: 193.47 um ± SEM: 6.673 um) versus (154.16 um ± 9.95 um) in control, p < 0.001. Pre-treatment with β-HB, SCFA receptor inhibitor, hindered neurosphere expansion (p < 0.001). While hNSCs spontaneously differentiated to (48.38% ± 6.08%) neurons (Tubulin-IIIβ positive) and (46.63% ± 2.5%) glia (GFAP positive), PPA treatment drastically shifted differentiation to 80% GFAP cells (p < 0.05). Following 2 mM PPA exposure, TNF-α transcription increased 4.98 fold and the cytokine increased 3.29 fold compared to control (P < 0.001). Likewise, GPR41 (PPA receptor) and pro-survival p-Akt protein were elevated (p < 0.001). PTEN (Akt inhibitor) level decreased to (0.42 ug/ul ± 0.04 ug/ul) at 2 mM PPA compared to (0.83 ug/ul ± 0.09 ug/ul) in control (p < 0.001). PPA at 2 mM decreased neurite outgrowth to (80.70 um ± 5.5 um) compared to (194.93 um ± 19.7 um) in control. Clearly, the data supports a significant role for PPA in modulating hNSC patterning leading to gliosis, disturbed neuro-circuitry, and inflammatory response as seen in ASD.
Statins exacerbate glucose intolerance and hyperglycemia in a high sucrose fed rodent model
Authors: Seshadri Sriram , Rapaka Naimisha , Prajapati Bhumika , Mandaliya Dipeeka , Patel Sweta , Muggalla Christopher Shamir , Kapadia Bandish , Babu Phanithi Prakash , Misra Parimal , Saxena Uday 
Published: June 2019

AbstractStatins are first-line therapy drugs for cholesterol lowering. While they are highly effective at lowering cholesterol, they have propensity to induce hyperglycemia in patients. Only limited studies have been reported which studied the impact of statins on (a) whether they can worsen glucose tolerance in a high sucrose fed animal model and (b) if so, what could be the molecular mechanism. We designed studies using high sucrose fed animals to explore the above questions. The high sucrose fed animals were treated with atorvastatin and simvastatin, the two most prescribed statins. We examined the effects of statins on hyperglycemia, glucose tolerance, fatty acid accumulation and insulin signaling. We found that chronic treatment with atorvastatin made the animals hyperglycemic and glucose intolerant in comparison with diet alone. Treatment with both statins lead to fatty acid accumulation and inhibition of insulin signaling in the muscle tissue at multiple points in the pathway.
Enhanced Efficiency of Carbon-Based Mesoscopic Perovskite Solar Cells through a Tungsten Oxide Nanoparticle Additive in the Carbon Electrode
Authors: Zhou Lin , Zuo Yuhua , Mallick Tapas Kumar , Sundaram Senthilarasu 
Published: June 2019

AbstractThis paper presents perovskite solar cells employed with WO3 nanoparticles embedded carbon top electrode. WO3 nanoparticles works as an inorganic hole-transport material (HTM) to promote the hole-extraction in the perovskite/carbon interface as revealed by efficiency, electrochemical impedance and external quantum efficiency measurements. As a result, a 40% enhancement of energy conversion efficiency has been achieved compared to the reference devices with the energy conversion efficiency of 10.77% under standard conditions. In addition, the Li-TFSI can modify the interface between electron-transport material (ETM) and perovskite, which may inhibit the recombination at the ETM/perovskite interface. The VOC of devices upon the modification of Li-TFSI is increased from 887.9 to 934.2 mV. This work highlights about the enlightenment of the effective performance of carbon-based mesoscopic PSCs by the introduction of HTM and the modification of interfaces.
Identifying niche and fitness dissimilarities in invaded marine macroalgal canopies within the context of contemporary coexistence theory
Authors: Epstein Graham , Hawkins Stephen J. , Smale Dan A. 
Published: June 2019

AbstractContemporary coexistence theory provides a framework for predicting invasiveness and impact of Invasive Non-Native Species (INNS) by incorporating differences in niche and fitness between INNS and co-occurring native species. The widespread invasive kelpUndaria pinnatifidais considered a high-risk INNS, although a robust evidence base regarding its invasiveness and impact is lacking in many regions. Invaded macroalgal canopies at nine coastal sites in the southwest UK were studied over three years to discern whetherUndariais coexisting or competing with native canopy-forming species across different habitat types. Spatial, temporal and depth-related trends in species distributions and abundance were recorded within intertidal and subtidal rocky reef as well as on marina pontoons. A primary succession experiment also examined competitive interactions between species. In rocky reef habitats,Undariahad lower fitness compared to long-lived native perennials, but was able to coexist due to niche dissimilarity between species. In contrast,Undariawas likely to be competing with short-lived native annuals on rocky reef due to large niche overlap and similar fitness. In marina habitats,Undariadominated over all other canopy formers due to low niche diversification and higher fitness. Generalisations on INNS impact cannot be made across habitats or species, without considering many abiotic factors and biotic interactions.
Non-conventional graphene superlattices as electron band-pass filters
Authors: Sánchez-Arellano A. , Madrigal-Melchor J. , Rodríguez-Vargas I. 
Published: June 2019

AbstractElectron transmission through different non-conventional (non-uniform barrier height) gated and gapped graphene superlattices (GSLs) is studied. Linear, Gaussian, Lorentzian and Pöschl-Teller superlattice potential profiles have been assessed. A relativistic description of electrons in graphene as well as the transfer matrix method have been used to obtain the transmission properties. We find that it is not possible to have perfect or nearly perfect pass bands in gated GSLs. Regardless of the potential profile and the number of barriers there are remanent oscillations in the transmission bands. On the contrary, nearly perfect pass bands are obtained for gapped GSLs. The Gaussian profile is the best option when the number of barriers is reduced, and there is practically no difference among the profiles for large number of barriers. We also find that both gated and gapped GSLs can work as omnidirectional band-pass filters. In the case of gated Gaussian GSLs the omnidirectional range goes from −50° to 50° with an energy bandwidth of 55 meV, while for gapped Gaussian GSLs the range goes from −80° to 80° with a bandwidth of 40 meV. Here, it is important that the energy range does not include remanent oscillations. On the light of these results, the hole states inside the barriers of gated GSLs are not beneficial for band-pass filtering. So, the flatness of the pass bands is determined by the superlattice potential profile and the chiral nature of the charge carriers in graphene. Moreover, the width and the number of electron pass bands can be modulated through the superlattice structural parameters. We consider that our findings can be useful to design electron filters based on non-conventional GSLs.
Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control
Authors: Zuo Jinhua , Wang Yunxiang , Zhu Benzhong , Luo Yunbo , Wang Qing , Gao Lipu 
Published: June 2019

AbstractPepper is an important vegetable worldwide and is a model plant for nonclimacteric fleshy fruit ripening. Drastic visual changes and internal biochemical alterations are involved in fruit coloration, flavor, texture, aroma, and palatability to animals during the pepper fruit ripening process. To explore the regulation of bell pepper fruit ripening by noncoding RNAs (ncRNAs), we examined their expression profiles; 43 microRNAs (miRNAs), 125 circular RNAs (circRNAs), 366 long noncoding RNAs (lncRNAs), and 3266 messenger RNAs (mRNAs) were differentially expressed (DE) in mature green and red ripe fruit. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the targets of the DE ncRNAs and DE mRNAs included several kinds of transcription factors (TFs) (ERF, bHLH, WRKY, MYB, NAC, bZIP, and ARF), enzymes involved in cell wall metabolism (beta-galactosidase, beta-glucosidase, beta-amylase, chitinase, pectate lyase (PL), pectinesterase (PE) and polygalacturonase (PG)), enzymes involved in fruit color accumulation (bifunctional 15-cis-phytoene synthase, 9-cis-epoxycarotenoid dioxygenase, beta-carotene hydroxylase and carotene epsilon-monooxygenase), enzymes associated with fruit flavor and aroma (glutamate-1-semialdehyde 2,1-aminomutase, anthocyanin 5-aromatic acyltransferase, and eugenol synthase 1) and enzymes involved in the production of ethylene (ET) (ACO1/ACO4) as well as other plant hormones such as abscisic acid (ABA), auxin (IAA), and gibberellic acid (GA). Based on accumulation profiles, a network of ncRNAs and mRNAs associated with bell pepper fruit ripening was developed that provides a foundation for further developing a more refined understanding of the molecular biology of fruit ripening.
Neighbourhood socioeconomic deprivation and allostatic load: a multi-cohort study
Authors: Ribeiro Ana Isabel , Fraga Silvia , Kelly-Irving Michelle , Delpierre Cyrille , Stringhini Silvia , Kivimaki Mika , Joost Stéphane , Guessous Idris , Gandini Martina , Vineis Paolo , Barros Henrique 
Published: June 2019

AbstractLiving in deprived neighbourhoods may have biological consequences, but few studies have assessed this empirically. We examined the association between neighbourhood deprivation and allostatic load, a biological marker of wear and tear, taking into account individual’s socioeconomic position. We analysed data from three cohort studies (CoLaus-Switzerland; EPIPorto-Portugal; Whitehall II-UK) comprising 16,364 participants. We defined allostatic load using ten biomarkers of dysregulated metabolic, cardiovascular, and inflammatory systems (body mass index; waist circumference; total, high and low density lipoprotein cholesterol; triglycerides; glucose; systolic and diastolic blood pressure; C-reactive protein). Mixed Poisson regression models were fitted to examine associations with neighbourhood deprivation (in quintiles, Q1-least deprived as reference). After adjustment for confounding variables, participants living in the most deprived quintile had 1.13 times higher allostatic load than those living in the least deprived quintile (Relative Risk, RR, for Q2 RR = 1.06, 95% CI 1.03-1.09; Q3 = 1.06, 1.03–1.10; Q4 = 1.09, 1.06–1.12; Q5 = 1.13, 1.09–1.16). This association was partially modified by individual’s socioeconomic position, such that the relative risk was higher in participants with low socioeconomic position (Q5 vs Q1 1.16, 1.11–1.22) than those with high socioeconomic position (Q5 vs Q1 1.07, 1.01–1.13). Neighbourhood deprivation is associated with biological wear and tear, suggesting that neighbourhood-level interventions may yield health gains.