bluuebunny/crossref_metadata_2025_split huggingface dataset:
A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome
Authors: Misselbeck Karla , Parolo Silvia , Lorenzini Francesca , Savoca Valeria , Leonardelli Lorena , Bora Pranami , Morine Melissa J. , Mione Maria Caterina , Domenici Enrico , Priami Corrado 
Published: November 2019

AbstractMetabolic syndrome is a pathological condition characterized by obesity, hyperglycemia, hypertension, elevated levels of triglycerides and low levels of high-density lipoprotein cholesterol that increase cardiovascular disease risk and type 2 diabetes. Although numerous predisposing genetic risk factors have been identified, the biological mechanisms underlying this complex phenotype are not fully elucidated. Here we introduce a systems biology approach based on network analysis to investigate deregulated biological processes and subsequently identify drug repurposing candidates. A proximity score describing the interaction between drugs and pathways is defined by combining topological and functional similarities. The results of this computational framework highlight a prominent role of the immune system in metabolic syndrome and suggest a potential use of the BTK inhibitor ibrutinib as a novel pharmacological treatment. An experimental validation using a high fat diet-induced obesity model in zebrafish larvae shows the effectiveness of ibrutinib in lowering the inflammatory load due to macrophage accumulation.
The genomic footprint of sexual conflict
Authors: Sayadi Ahmed , Martinez Barrio Alvaro , Immonen Elina , Dainat Jacques , Berger David , Tellgren-Roth Christian , Nystedt Björn , Arnqvist Göran 
Published: November 2019

AbstractGenes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic ‘tug-of-war’ between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetleCallosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.
PTBP1-mediated regulation of AXL mRNA stability plays a role in lung tumorigenesis
Authors: Cho Chun-Yu , Chung Shih-Ying , Lin Shankung , Huang Jhy-Shrian , Chen Yen-Lin , Jiang Shih-Sheng , Cheng Li-Chun , Kuo Tsu-Hsiang , Lay Jong-Ding , Yang Ya-Yu , Lai Gi-Ming , Chuang Shuang-En 
Published: November 2019

AbstractAXL is expressed in many types of cancer and promotes cancer cell survival, metastasis and drug resistance. Here, we focus on identifying modulators that regulate AXL at the mRNA level. We have previously observed that the AXL promoter activity is inversely correlated with the AXL expression levels, suggesting that post-transcriptional mechanisms exist that down-regulate the expression of AXL mRNA. Here we show that the RNA binding protein PTBP1 (polypyrimidine tract-binding protein) directly targets the 5′-UTR of AXL mRNA in vitro and in vivo. Moreover, we also demonstrate that PTBP1, but not PTBP2, inhibits the expression of AXL mRNA and the RNA recognition motif 1 (RRM1) of PTBP1 is crucial for this interaction. To clarify how PTBP1 regulates AXL expression at the mRNA level, we found that, while the transcription rate of AXL was not significantly different, PTBP1 decreased the stability of AXL mRNA. In addition, over-expression of AXL may counteract the PTBP1-mediated apoptosis. Knock-down of PTBP1 expression could enhance tumor growth in animal models. Finally, PTBP1 was found to be negatively correlated with AXL expression in lung tumor tissues in Oncomine datasets and in tissue micro-array (TMA) analysis. In conclusion, we have identified a molecular mechanism of AXL expression regulation by PTBP1 through controlling the AXL mRNA stability. These findings may represent new thoughts alternative to current approaches that directly inhibit AXL signaling and may eventually help to develop novel therapeutics to avoid cancer metastasis and drug resistance.
Vector competence of Aedes aegypti and Culex quinquefasciatus from the metropolitan area of Guadalajara, Jalisco, Mexico for Zika virus
Authors: Elizondo-Quiroga Darwin , Ramírez-Medina Miriam , Gutiérrez-Ortega Abel , Elizondo-Quiroga Armando , Muñoz-Medina José Esteban , Sánchez-Tejeda Gustavo , González-Acosta Cassandra , Correa-Morales Fabián 
Published: November 2019

AbstractZika virus (ZIKV) is a mosquito-borne pathogen discovered in the late 40’s in Uganda during a surveillance program for yellow fever. By 2014 the virus reached Eastern Island in the Americas, and two years later, the virus spread to almost all countries and territories of the Americas. The mosquito Aedes aegypti has been identified as the main vector of the disease, and several researchers have also studied the vector competence of Culex quinquefasciatus in virus transmission. The aim of the present study was to evaluate the vector competence of Ae. aegypti and Cx. quinquefasciatus in order to understand their roles in the transmission of ZIKV in Guadalajara, Jalisco, Mexico. In blood feeding laboratry experiments, we found that Ae. aegypti mosquitoes showed to be a competent vector able to transmit ZIKV in this area. On the other hand, we found that F0 Cx. quinquefasciatus mosquitoes are refractory to ZIKV infection, dissemination and transmission.
Identification of novel predictive factors for post surgical corneal haze
Authors: Kumar Nimisha R. , Khamar Pooja , Shetty Rohit , Sharma Ankit , Shetty Naren , Pahuja Natasha , Abilash Valsala Gopalakrishnan , Jhanji Vishal , Ghosh Anuprita , Mohan Rajiv R. , Vangala Rajani Kanth , Ghosh Arkasubhra 
Published: November 2019

AbstractMolecular factors altered in corneas that develop haze post refractive surgery have been described, but pre-existing factors that predispose clinically normal corneas to aberrant fibrosis post surgery and the role of the corneal epithelium remains unknown. We analyzed the global gene expression in epithelium collected intraoperatively from subjects undergoing photorefractive keratectomy. Subjects were grouped into those that developed haze 12 months post surgery (n = 6 eyes; haze predisposed) and those that did not develop haze in a similar follow up duration (n = 11 eyes; controls). Ontological analysis of 1100 upregulated and 1780 downregulated genes in the haze predisposed group revealed alterations in pathways associated with inflammation, wnt signaling, oxidative stress, nerve functions and extra cellular matrix remodeling. Novel factors such as PREX1, WNT3A, SOX17, GABRA1and PXDN were found to be significantly altered in haze predisposed subjects and those with active haze(n = 3), indicating their pro-fibrotic role. PREX1 was significantly upregulated in haze predisposed subjects. Ectopic expression of PREX1 in cultured human corneal epithelial cells enhanced their rate of wound healing while its ablation using shRNA reduced healing compared to matched controls. Recombinant TGFβ treatment in PREX1 overexpressing corneal cells led to enhanced αSMA expression and Vimentin phosphorylation while the converse was true for shPREX1 expressing cells. Our data identify a few novel factors in the corneal epithelium that may define a patient’s risk to developing post refractive corneal haze.
Breakdown of Scaling and Friction Weakening in Intermittent Granular Flow
Authors: Baldassarri A. , Annunziata M. A. , Gnoli A. , Pontuale G. , Petri A. 
Published: November 2019

AbstractMany materials are produced, processed and stored as grains, while granularity of matter can be crucial in triggering potentially catastrophic geological events like landslides, avalanches and earthquakes. The response of grain assemblies to shear stress is therefore of utmost relevance to both human and natural environment. At low shear rate a granular system flows intermittently by distinct avalanches. In such state the avalanche velocity in time is expected to follow a symmetrical and universal average behavior, whose dependence on the slip size reduces to a scale factor. Analyzing data from long lasting experiments, we observe a breakdown of this scaling: While in short slips velocity shows indeed a self-similar and symmetric profile, it does not in long slips. The investigation of frictional response in these different regimes evidences that this breakdown can be traced back to the onset of a friction weakening, which is of dynamical origin and can amplify instabilities exactly in this critical state, the most frequent state for natural hazards.
Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
Authors: Gardner Joseph J. , Hodge Bri-Mathias S. , Boyle Nanette R. 
Published: November 2019

AbstractIn natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in ‘ideal’ laboratory environments, cells can experience a high degree of heterogeneity in their environments. Unfortunately, most of the metabolic modeling approaches that are currently used assume ideal conditions and that each cell is identical, limiting their application to pure cultures in well-mixed vessels. Here we describe our development of Multiscale Multiobjective Systems Analysis (MiMoSA), a metabolic modeling approach that can track individual cells in both space and time, track the diffusion of nutrients and light and the interaction of cells with each other and the environment. As a proof-of concept study, we used MiMoSA to model the growth of Trichodesmium erythraeum, a filamentous diazotrophic cyanobacterium which has cells with two distinct metabolic modes. The use of MiMoSA significantly improves our ability to predictively model metabolic changes and phenotype in more complex cell cultures.
Glacial Indonesian Throughflow weakening across the Mid-Pleistocene Climatic Transition
Authors: Petrick Benjamin , Martínez-García Alfredo , Auer Gerald , Reuning Lars , Auderset Alexandra , Deik Hanaa , Takayanagi Hideko , De Vleeschouwer David , Iryu Yasufumi , Haug Gerald H. 
Published: November 2019

AbstractThe Indonesian Throughflow (ITF) controls the oceanic flux of heat and salt between the Pacific and Indian Oceans and therewith plays an important role in modulating the meridional overturning circulation and low latitude hydrological cycle. Here, we report new sea surface temperature and aridity records from the west coast of Australia (IODP Site U1460), which allow us to assess the sensitivity of the eastern Indian Ocean to the major reorganization of Earth’s climate that occurred during the Mid-Pleistocene Transition. Our records indicate glacial coolings at 1.55 and 0.65 million years ago that are best explained by a weakening of the ITF as a consequence of global sea level and tectonic changes. These coincide with the development of pronounced gradients in the carbon isotope composition of the different ocean basins and with substantial changes in regional aridity, suggesting that the restrictions of the ITF influenced both the evolution of global ocean circulation and the development of the modern hydrological cycle in Western Australia.
Highly Luminescent Ternary Nanocomposite of Polyaniline, Silver Nanoparticles and Graphene Oxide Quantum Dots
Authors: Shokry Azza , Khalil M. M. A. , Ibrahim Hesham , Soliman Moataz , Ebrahim Shaker 
Published: November 2019

AbstractQuantum dots (QDs) with photostability show a potential application in optical sensing and biological imaging. In this work, ternary nanocomposite (NC) of high fluorescent polyaniline (PANI)/2-acrylamido-2-methylpropanesulfonic acid (AMPSA) capped silver nanoparticles (NPs)/graphene oxide quantum dots (PANI/Ag (AMPSA)/GO QDs) have been synthesized by in situ chemical oxidative polymerization of aniline in the presence of Ag (AMPSA) NPs and GO QDs. Ag (AMPSA) NPs and GO QDs were prepared by AgNO3 chemical reduction and glucose carbonization methods, respectively. The prepared materials were characterized using UV-visible, Fourier transform infrared (FTIR), photoluminescence and Raman spectroscopies, X-Ray diffractometer (XRD) and high- resolution transmission electron microscopy (HRTEM). HRTEM micrographs confirmed the preparation of GO QDs with an average size of 15 nm and Ag (AMPSA) NPs with an average size of 20 nm. PANI/Ag (AMPSA)/GO QDs NC showed high and stable emission peak at 348 nm. This PANI/Ag (AMPSA)/GO QDs NC can emerge as a new class of fluorescence materials that could be suitable for practical sensing applications.
Effect of biochar addition on leaf-litter decomposition at soil surface during three years in a warm-temperate secondary deciduous forest, Japan
Authors: Minamino Yukiya , Fujitake Nobuhide , Suzuki Takeshi , Yoshitake Shinpei , Koizumi Hiroshi , Tomotsune Mitsutoshi 
Published: November 2019

AbstractThe addition of biochar to the forest floor should facilitate efficient carbon sequestration. However, little is known about how biochar addition effects litter decomposition, which is related to carbon and nutrient dynamics in forest ecosystems. This study evaluated the effect of biochar addition on leaf litter decomposition in a forest ecosystem. To examine whether leaf litter decomposition was stimulated above and below biochar, litterbag experiments were carried out for about 3 years in a field site where biochar was added at the rate of 0, 5 and 10 t ha−¹ (C0, C5 and C10 plots) to the forest floor in a temperate oak forest, Japan. Biochar addition at C10 significantly enhanced litter decomposition below biochar for 2 years after treatment and above biochar for 1 year after treatment. Litter water content in biochar plots tended to increase under dry conditions. Biochar addition enhanced litter decomposition because of increased microbial activity with increased moisture content and accelerated the decomposition progress rather than changing the decomposition pattern. However, the carbon emission through changing leaf litter decomposition was small when compared with the carbon addition by biochar, indicating that biochar could be an effective material for carbon sequestration in forest ecosystems.
Two-dimensional layered magnesium–cobalt hydroxide crochet structure for high rate and long stable supercapacitor application
Authors: Nanwani Alisha , Deshmukh Kavita A. , Sivaraman P. , Peshwe D. R. , Sharma Indu , Dhoble S. J. , Swart H. C. , Deshmukh Abhay D. , Gupta Bipin Kumar 
Published: November 2019

AbstractPseudocapacitors with nickel/cobalt hydroxide-based electrodes show promises energy storage devices, because they are economical and safe, but cycle stability and high current rate capability have not been achieved. We shed light on how magnesium in double-layered hydroxides serves as a supercapacitor electrode in optimal environments. Here we show the high rate capability and long-term stability of layered magnesium–cobalt double hydroxide (L-MCH) electrodes, which is superior to existing electrodes. The pseudocapacitor made with Mg2+ and Co2+ double hydroxide as active materials, does not have an intricate fabrication process. The L-MCH pseudocapacitor has a specific capacitance comparable to most double hydroxide-based materials and capacity retention greater than 107% over 10,000 cycles, which is in line with commercial devices. Our proposed method also offers a much faster and reliable route for electrode fabrication, which could result in the development of a new generation of supercapacitors, batteries and hybrid devices.
Acceleration of superrotation in simulated hot Jupiter atmospheres
Authors: Debras F. , Mayne N. , Baraffe I. , Jaupart E. , Mourier P. , Laibe G. , Goffrey T. , Thuburn J. 
Published: November 2019

Context. Atmospheric superrotating flows at the equator are a nearly ubiquitous result when conducting simulations of hot Jupiters. One theory explaining how this zonally-coherent flow reaches equilibrium has already been developed in the literature. This understanding, however, relies on the existence of either an initial superrotating flow or a sheared flow, coupled with a slow evolution that permits a linear steady state to be reached.
Aims. A consistent physical understanding of superrotation is needed for arbitrary drag and radiative timescales, along with the relevance of taking linear steady states into account, needs to be assessed.
Methods. We obtained an analytical expression for the structure, frequency, and decay rate of propagating waves in hot Jupiter atmospheres around a state at rest in the 2D shallow-water β-plane limit. We solved this expression numerically and confirmed the robustness of our results with a 3D linear wave algorithm. We then compared it with 3D simulations of hot Jupiter atmospheres and studied the nonlinear momentum fluxes.
Results. We show that under strong day-night heating, the dynamics do not transit through a linear steady state when starting from an initial atmosphere in solid body rotation. We further demonstrate that nonlinear effects favor the initial spin-up of superrotation and that acceleration due to the vertical component of the eddy-momentum flux is critical to the initial development of superrotation.
Conclusions. We describe the initial phases of the acceleration of superrotation, including the consideration of differing radiative and drag timescales, and we conclude that eddy-momentum-driven superrotating equatorial jets are robust, physical phenomena in simulations of hot Jupiter atmospheres.
Tumorrisiken nach Organtransplantation
Authors: Thorban Stefan , Matevossian Edouard 
Published: November 2019

ZusammenfassungSeit Beginn der Organtransplantation in Deutschland vor fast 40 Jahren steigt die Zahl der Langzeittransplantierten und damit das Tumorrisiko für die Empfänger. Tumorgenese und Tumorinzidenz bei verschiedenen Tumorentitäten werden insbesondere unter dem Aspekt der Langzeitimmunsuppression untersucht. Notwendige Screeningverfahren, Prävention und Risikofaktoren bei den einzelnen Tumortypen werden analysiert sowie Therapieempfehlungen untersucht. Im Gespräch mit dem Patienten sind der Verlust der Lebensqualität mit einem möglichem Transplantatverlust unter der Therapie gegenüber der zu erwartenden Lebenserwartung zu erörtern.
Extremitätentransplantation
Authors: Enechukwu Anieto Onochie Matthias , Mett Tobias R. , Vogt Peter M. , Krezdorn Nicco 
Published: November 2019

ZusammenfassungDie Entwicklung der letzten 20 Jahre hat die technischen wie immunologischen Voraussetzungen geschaffen, komplexe Rekonstruktionen amputierter Extremitäten mittels allogener Transplantation möglich zu machen. Dabei sind diese Eingriffe inzwischen aus dem Stadium eines experimentellen therapeutischen Eingriffs zu einer klinisch etablierten Rekonstruktionsmöglichkeit erwachsen. Aufgrund der lebensqualitätsspendenden, aber nicht lebensrettenden Natur dieser Eingriffe müssen die möglichen Risiken und Komplikationen, die aus einem solchen Eingriff erwachsen, sowie der lebenslang notwendigen Immunsuppression, kritisch und individuell evaluiert werden. Aus diesem Grund ist die Indikation auch nur bei Patienten mit bilateraler Verletzung zu stellen. Eine erfolgreiche Transplantation kann den Patienten jedoch dann eine deutliche Verbesserung der sensorischen und motorischen Fähigkeiten mit relevanter Verbesserung der Lebensqualität ermöglichen und sollte daher als Therapieoption bei selektiven Patienten mitbedacht werden.
Immunoglobulin G4 (IgG4)-related disease of the stomach – a challenging differential diagnosis in suspected gastric cancer
Authors: Probst Andreas , Schaller Tina , Sommer Florian , Geissler Bernd , Agaimy Abbas , Messmann Helmut , Märkl Bruno 
Published: November 2019

Abstract
Background Immunoglobulin G4-related disease (IgG4-RD) can involve different organs and is diagnosed by a combination of clinicopathological features, including storiform fibrosclerosis infiltrated by numerous IgG4-positive plasma cells that frequently forms tumor-like lesions with or without associated obliterative phlebitis. Involvement of the stomach is rare and can occur as part of a multiorgan involvement of IgG4-RD or as isolated gastric involvement.
Case report We report 2 female patients with therapy-refractory gastric ulcers associated with gastric wall thickening and lymphadenopathy that were highly suggestive of gastric cancer or lymphoma. Biopsies failed to confirm a diagnosis, and IgG4-RD was diagnosed only after surgical resection in both patients. The previous literature on gastric IgG4-RD is summarized and shows different characteristics in patients with multiorgan IgG4-RD and isolated gastric IgG4-RD. As reported for autoimmune pancreatitis type 1, patients with multiorgan IgG4-RD are mainly elderly men with frequently elevated serum IgG4 concentrations. In contrast, isolated gastric IgG4-RD predominantly affects female patients with normal serum IgG4 levels. Surgical resection is commonly performed due to the clinical suspicion of malignancy and the absence of findings indicative of IgG4-RD on biopsy. Today, diagnosis is confirmed histopathologically only after resection.
Conclusion IgG4-RD should be taken into account when gastric malignancy is suspected endoscopically or radiologically and biopsies fail to confirm the presence of a malignancy (especially subepithelial tumors or refractory gastric ulcers). Serum IgG4 concentrations are insufficient to confirm localized gastric IgG4-RD. Diagnostic workups need to be improved to avoid unnecessary surgical resections with the attendant potential morbidity and mortality.
Laccaridione C, a Bioactive Polyketide from the Fungus
Montagnula sp.
Authors: Almeida Celso , Mackenzie Thomas Andrew , González-Menéndez Víctor , de Pedro Nuria , Pérez-Victoria Ignacio , Crespo Gloria , Martín Jesús , Genilloud Olga , Vicente Francisca , Cautain Bastien , Reyes Fernando 
Published: November 2019

AbstractThe new polyketide laccaridione C (1) was obtained by bioassay-guided
isolation of organic extracts of the fungal strain CF-223743, isolated from dung
collected in a forest of Grand Comoros Island. Its structure was established
using spectroscopic methods, namely HRMS and 1D and 2D NMR. The new compound was
tested against seven cancer cell lines, evidencing effective activity against
melanoma (A2058) with an IC50 of 13.2 µM, and an
increased activity against breast cancer (MCF-7) with an IC50 of
3.7 µM. The strain CF-223743 was taxonomically identified as
Montagnula sp. based on ITS/28S analysis