bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling the Re effect in Ni-based single crystal superalloys
Authors: Wu Xiaoxiang , Makineni Surendra Kumar , Liebscher Christian H. , Dehm Gerhard , Rezaei Mianroodi Jaber , Shanthraj Pratheek , Svendsen Bob , Bürger David , Eggeler Gunther , Raabe Dierk , Gault Baptiste 
Published: January 2020

AbstractSingle crystal Ni-based superalloys have long been an essential material for gas turbines in aero engines and power plants due to their outstanding high temperature creep, fatigue and oxidation resistance. A turning point was the addition of only 3 wt.% Re in the second generation of single crystal Ni-based superalloys which almost doubled the creep lifetime. Despite the significance of this improvement, the mechanisms underlying the so-called “Re effect” have remained controversial. Here, we provide direct evidence of Re enrichment to crystalline defects formed during creep deformation, using combined transmission electron microscopy, atom probe tomography and phase field modelling. We reveal that Re enriches to partial dislocations and imposes a drag effect on dislocation movement, thus reducing the creep strain rate and thereby improving creep properties. These insights can guide design of better superalloys, a quest which is key to reducing CO2 emissions in air-traffic.
Scalable photonic sources using two-dimensional lead halide perovskite superlattices
Authors: Jagielski Jakub , Solari Simon F. , Jordan Lucie , Scullion Declan , Blülle Balthasar , Li Yen-Ting , Krumeich Frank , Chiu Yu-Cheng , Ruhstaller Beat , Santos Elton J. G. , Shih Chih-Jen 
Published: January 2020

AbstractMiniaturized photonic sources based on semiconducting two-dimensional (2D) materials offer new technological opportunities beyond the modern III-V platforms. For example, the quantum-confined 2D electronic structure aligns the exciton transition dipole moment parallel to the surface plane, thereby outcoupling more light to air which gives rise to high-efficiency quantum optics and electroluminescent devices. It requires scalable materials and processes to create the decoupled multi-quantum-well superlattices, in which individual 2D material layers are isolated by atomically thin quantum barriers. Here, we report decoupled multi-quantum-well superlattices comprised of the colloidal quantum wells of lead halide perovskites, with unprecedentedly ultrathin quantum barriers that screen interlayer interactions within the range of 6.5 Å. Crystallographic and 2Dk-space spectroscopic analysis reveals that the transition dipole moment orientation of bright excitons in the superlattices is predominantly in-plane and independent of stacking layer and quantum barrier thickness, confirming interlayer decoupling.
Phenotypic changes of HER2-positive breast cancer during and after dual HER2 blockade
Authors: Brasó-Maristany Fara , Griguolo Gaia , Pascual Tomás , Paré Laia , Nuciforo Paolo , Llombart-Cussac Antonio , Bermejo Begoña , Oliveira Mafalda , Morales Serafín , Martínez Noelia , Vidal Maria , Adamo Barbara , Martínez Olga , Pernas Sonia , López Rafael , Muñoz Montserrat , Chic Núria , Galván Patricia , Garau Isabel , Manso Luis , Alarcón Jesús , Martínez Eduardo , Gregorio Sara , Gomis Roger R. , Villagrasa Patricia , Cortés Javier , Ciruelos Eva , Prat Aleix 
Published: January 2020

AbstractThe HER2-enriched (HER2-E) subtype within HER2-positive (HER2+) breast cancer is highly addicted to the HER2 pathway. However, ∼20–60% of HER2+/HER2-E tumors do not achieve a complete response following anti-HER2 therapies. Here we evaluate gene expression data before, during and after neoadjuvant treatment with lapatinib and trastuzumab in HER2+/HER2-E tumors of the PAMELA trial and breast cancer cell lines. Our results reveal that dual HER2 blockade in HER2-E disease induces a low-proliferative Luminal A phenotype both in patient’s tumors and in vitro models. These biological changes are more evident in hormone receptor-positive (HR+) disease compared to HR-negative disease. Interestingly, increasing the luminal phenotype with anti-HER2 therapy increased sensitivity to CDK4/6 inhibition. Finally, discontinuation of HER2-targeted therapy in vitro, or acquired resistance to anti-HER2 therapy, leads to restoration of the original HER2-E phenotype. Our findings support the use of maintenance anti-HER2 therapy and the therapeutic exploitation of subtype switching with CDK4/6 inhibition.
Androgen deprivation upregulates SPINK1 expression and potentiates cellular plasticity in prostate cancer
Authors: Tiwari Ritika , Manzar Nishat , Bhatia Vipul , Yadav Anjali , Nengroo Mushtaq A. , Datta Dipak , Carskadon Shannon , Gupta Nilesh , Sigouros Michael , Khani Francesca , Poutanen Matti , Zoubeidi Amina , Beltran Himisha , Palanisamy Nallasivam , Ateeq Bushra 
Published: January 2020

AbstractEmergence of an aggressive androgen receptor (AR)-independent neuroendocrine prostate cancer (NEPC) after androgen-deprivation therapy (ADT) is well-known. Nevertheless, the majority of advanced-stage prostate cancer patients, including those with SPINK1-positive subtype, are treated with AR-antagonists. Here, we show AR and its corepressor, REST, function as transcriptional-repressors of SPINK1, and AR-antagonists alleviate this repression leading to SPINK1 upregulation. Increased SOX2 expression during NE-transdifferentiation transactivates SPINK1, a critical-player for maintenance of NE-phenotype. SPINK1 elicits epithelial-mesenchymal-transition, stemness and cellular-plasticity. Conversely, pharmacological Casein Kinase-1 inhibition stabilizes REST, which in cooperation with AR causes SPINK1 transcriptional-repression and impedes SPINK1-mediated oncogenesis. Elevated levels of SPINK1 and NEPC markers are observed in the tumors of AR-antagonists treated mice, and in a subset of NEPC patients, implicating a plausible role of SPINK1 in treatment-related NEPC. Collectively, our findings provide an explanation for the paradoxical clinical-outcomes after ADT, possibly due to SPINK1 upregulation, and offers a strategy for adjuvant therapies.
Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles
Authors: Kalnins Gints , Cesle Eva-Emilija , Jansons Juris , Liepins Janis , Filimonenko Anatolij , Tars Kaspars 
Published: January 2020

AbstractBacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from theKlebsiella pneumoniaeGRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
High-resolution and bias-corrected CMIP5 projections for climate change impact assessments
Authors: Navarro-Racines Carlos , Tarapues Jaime , Thornton Philip , Jarvis Andy , Ramirez-Villegas Julian 
Published: January 2020

AbstractProjections of climate change are available at coarse scales (70–400 km). But agricultural and species models typically require finer scale climate data to model climate change impacts. Here, we present a global database of future climates developed by applying the delta method –a method for climate model bias correction. We performed a technical evaluation of the bias-correction method using a ‘perfect sibling’ framework and show that it reduces climate model bias by 50–70%. The data include monthly maximum and minimum temperatures and monthly total precipitation, and a set of bioclimatic indices, and can be used for assessing impacts of climate change on agriculture and biodiversity. The data are publicly available in the World Data Center for Climate (WDCC; cera-www.dkrz.de), as well as in the CCAFS-Climate data portal (http://ccafs-climate.org). The database has been used up to date in more than 350 studies of ecosystem and agricultural impact assessment.
Metabolomic and Lipidomic Signatures of Metabolic Syndrome and its Physiological Components in Adults: A Systematic Review
Authors: Monnerie Stéphanie , Comte Blandine , Ziegler Daniela , Morais José A. , Pujos-Guillot Estelle , Gaudreau Pierrette 
Published: January 2020

AbstractThe aim of this work was to conduct a systematic review of human studies on metabolite/lipid biomarkers of metabolic syndrome (MetS) and its components, and provide recommendations for future studies. The search was performed in MEDLINE, EMBASE, EMB Review, CINHAL Complete, PubMed, and on grey literature, for population studies identifying MetS biomarkers from metabolomics/lipidomics. Extracted data included population, design, number of subjects, sex/gender, clinical characteristics and main outcome. Data were collected regarding biological samples, analytical methods, and statistics. Metabolites were compiled by biochemical families including listings of their significant modulations. Finally, results from the different studies were compared. The search yielded 31 eligible studies (2005–2019). A first category of articles identified prevalent and incident MetS biomarkers using mainly targeted metabolomics. Even though the population characteristics were quite homogeneous, results were difficult to compare in terms of modulated metabolites because of the lack of methodological standardization. A second category, focusing on MetS components, allowed comparing more than 300 metabolites, mainly associated with the glycemic component. Finally, this review included also publications studying type 2 diabetes as a whole set of metabolic risks, raising the interest of reporting metabolomics/lipidomics signatures to reflect the metabolic phenotypic spectrum in systems approaches.
STF-62247 and pimozide induce autophagy and autophagic cell death in mouse embryonic fibroblasts
Authors: Kinzler Maximilian N. , Zielke Svenja , Kardo Simon , Meyer Nina , Kögel Donat , van Wijk Sjoerd J. L. , Fulda Simone 
Published: January 2020

AbstractInduction of autophagy can have beneficial effects in several human diseases, e.g. cancer and neurodegenerative diseases (ND). Here, we therefore evaluated the potential of two novel autophagy-inducing compounds, i.e. STF-62247 and pimozide, to stimulate autophagy as well as autophagic cell death (ACD) using mouse embryonic fibroblasts (MEFs) as a cellular model. Importantly, both STF-62247 and pimozide triggered several hallmarks of autophagy in MEFs, i.e. enhanced levels of LC3B-II protein, its accumulation at distinct cytosolic sites and increase of the autophagic flux. Intriguingly, autophagy induction by STF-62247 and pimozide resulted in cell death that was significantly reduced in ATG5- or ATG7-deficient MEFs. Consistent with ACD induction, pharmacological inhibitors of apoptosis, necroptosis or ferroptosis failed to protect MEFs from STF-62247- or pimozide-triggered cell death. Interestingly, at subtoxic concentrations, pimozide stimulated fragmentation of the mitochondrial network, degradation of mitochondrial proteins (i.e. mitofusin-2 and cytochrome c oxidase IV (COXIV)) as well as a decrease of the mitochondrial mass, indicative of autophagic degradation of mitochondria by pimozide. In conclusion, this study provides novel insights into the induction of selective autophagy as well as ACD by STF-62247 and pimozide in MEFs.
Information transfer through food from parents to offspring in wild Javan gibbons
Authors: Yi Yoonjung , Kim Yena , Hikmat Agus , Choe Jae C. 
Published: January 2020

AbstractThe adaptive functions of food transfer from parents to their offspring have been explained mainly by two mutually non-exclusive hypotheses: the nutritional and informational hypotheses. In this study, we examined the functions of food transfer in wild Javan gibbons (Hylobates moloch) by testing these hypotheses from both infants’ and mothers’ perspectives. We observed 83 cases of food solicitations that resulted in 54 occasions of food transfers in three groups over a 19-month period in Gunung Halimun-Salak National Park, Indonesia. Infants initiated all solicitations directed at their mothers with one solicitation towards a father. Food solicitation rate decreased as infant age increased and ceased before weaning. As predicted by the informational hypothesis, infants solicited more food items difficult to obtain and preferred by their parents. On the contrary to the nutritional hypothesis, infants solicited low-quality items more often than high-quality items. Mothers did not change probability of food transfer according to the food characteristics or infant age. Hence, our results suggest that the primary function of food transfer from mother to infant Javan gibbons seems to be information transfer rather than nutritional aids, similarly to great apes.
The evolutionary diversity of locomotor innovation in rodents is not linked to proximal limb morphology
Authors: Hedrick Brandon P. , Dickson Blake V. , Dumont Elizabeth R. , Pierce Stephanie E. 
Published: January 2020

AbstractRodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.
Forecasting high-dimensional dynamics exploiting suboptimal embeddings
Authors: Okuno Shunya , Aihara Kazuyuki , Hirata Yoshito 
Published: January 2020

AbstractDelay embedding—a method for reconstructing dynamical systems by delay coordinates—is widely used to forecast nonlinear time series as a model-free approach. When multivariate time series are observed, several existing frameworks can be applied to yield a single forecast combining multiple forecasts derived from various embeddings. However, the performance of these frameworks is not always satisfactory because they randomly select embeddings or use brute force and do not consider the diversity of the embeddings to combine. Herein, we develop a forecasting framework that overcomes these existing problems. The framework exploits various “suboptimal embeddings” obtained by minimizing the in-sample error via combinatorial optimization. The framework achieves the best results among existing frameworks for sample toy datasets and a real-world flood dataset. We show that the framework is applicable to a wide range of data lengths and dimensions. Therefore, the framework can be applied to various fields such as neuroscience, ecology, finance, fluid dynamics, weather, and disaster prevention.
Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics
Authors: Cooper Reilly O. , Cressler Clayton E. 
Published: January 2020

AbstractThe keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.
Investigation of fragmentation behaviours of isoquinoline alkaloids by mass spectrometry combined with computational chemistry
Authors: Qing Zhixing , Xu Yuqin , Yu Liuyi , Liu Jinghong , Huang Xiuqiong , Tang Zhaoshan , Cheng Pi , Zeng Jianguo 
Published: January 2020

AbstractIsoquinoline alkaloids, which are one of the most important types of alkaloids, are extensively distributed in herbal medicines. However, systematic and comprehensive investigations of the fragmentation behaviours of isoquinoline alkaloids have rarely been reported. Therefore, the goal of the present study is to simultaneously investigate the collision-induced dissociation patterns and the corresponding mechanism of isoquinoline alkaloids by mass spectrometry (MS) combined with computations. Nineteen types of isoquinoline alkaloids (66 compounds) were used as references to identify the characteristic fragmentation behaviours by quadrupole time-of-flight mass spectrometry (Q-TOF/MS) in positive electrospray ionization (ESI) mode. These types of isoquinoline alkaloids were divided into three categories primarily by the characteristic [M-NHR1R2]+ (R1 and R2 represent the substituent groups of the N-atom) fragment ions. High- and low-abundance [M-NHR1R2]+ ions were observed respectively for type I (1–13) and type II (14–29) alkaloids, respectively; however, the characteristic fragments were not detected for type III alkaloids (30–66) because of the existence of a p-π conjugated system. Each type of alkaloid was further classified by its characteristic fragmentation patterns and fragment ions. In addition, isoquinoline alkaloid with vicinal methoxy and hydroxy, vicinal methoxy, methylenedioxy, methoxy, and quaternary N-methyl groups could form the characteristic fragments by the loss of CH3OH, CH4, CH2O or CO, CH3 and CO, and CH3 moieties, respectively. The mechanisms of some interesting fragmentation behaviours, such as the formation of [M-NH3]+ and [M-CH3]+ fragment ions, were further demonstrated by computational chemistry. These characteristic fragmentation behaviours and fragment ions of isoquinoline alkaloids provide a solid foundation for the rapid and high-efficiency structural elucidation of similar metabolites in plant-derived medicines.
1.27 kW, 2.2 GHz pseudo-random binary sequence phase modulated fiber amplifier with Brillouin gain-spectrum overlap
Authors: Liu Meizhong , Yang Yifeng , Shen Hui , Zhang Jingpu , Zou Xingxing , Wang Hanbin , Yuan Lucheng , You Yang , Bai Gang , He Bing , Zhou Jun 
Published: January 2020

AbstractWe present a 2.2 GHz modulated, 1.27 kW output power, monolithic fiber amplifier based on pseudo-random binary sequence (PRBS) phase modulation. The spectral line spacing of maximizing the threshold enhancement factor (plateau of trend) was found by theoretical simulation. The spectral line spacing was adjusted to 12.7 MHz by a pattern length of n = 9, which is close to the plateau of trend in the proposed architecture. A 2.2 GHz low-pass radio frequency filter was used to control the FWHM of the seed. A four-stage Yb-doped fiber amplifier chain was established to boost a distributed Bragg reflector (DBR) laser and a distributed feedback (DFB) diode laser to 1.2 kW and 1.27 kW with a backward reflectively of <1‰, which shows a good suppression of SBS effect.
Conformational changes in Apolipoprotein N-acyltransferase (Lnt)
Authors: Wiseman Benjamin , Högbom Martin 
Published: January 2020

AbstractLipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three integral membrane enzymes. The last step of this process, unique to Gram-negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of Lnt from Escherichia coli. In one form we observe a highly dynamic arm that is able to restrict access to the active site as well as a covalent modification to the active site cysteine consistent with the thioester acyl-intermediate. In the second form, the enzyme crystallized in an open conformation exposing the active site to the environment. In total we observe 3 unique Lnt molecules that when taken together suggest the movement of essential loops and residues are triggered by substrate binding that could control the interaction between Lnt and the incoming substrate apolipoprotein. The results provide a dynamic context for residues shown to be central for Lnt function and provide further insights into its mechanism.
Green Reduction of Graphene Oxide using Kaffir Lime Peel Extract (Citrus hystrix) and Its Application as Adsorbent for Methylene Blue
Authors: Wijaya Ronald , Andersan Gracia , Permatasari Santoso Shella , Irawaty Wenny 
Published: January 2020

AbstractGreen reduction of graphene oxide (GO) by phytochemicals was explored using the aqueous extract of kaffir lime peels. The research methods included preparation of extracts, preparation of GO, preparation and characterization of reduced-GO (RGO) using Fourier Transform Infrared (FTIR), X-ray diffraction (XRD), and UV-Vis spectroscopy, as well as methylene blue (MB) adsorption test using RGO. The RGO characterization showed that GO was successfully reduced by a C=C group restoration. The MB adsorption kinetics profile in RGO is more suitable for the pseudo-second-order model, whereas for the adsorption isotherm it is more suitable for the Langmuir model with a maximum adsorption capacity (qmax) of 276.06 mg/g at room temperature. The best ratio of GO: kaffir lime peel extract used to prepare RGO was at a ratio of 1: 2. Based on the ΔG, ΔH, and ΔS values, the adsorption of RGO-MB was defined as spontaneous and endothermic process. The results promise the potential application of RGO derived via green route to remove cationic dye in wastewater.