bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-saturating quantum magnetization in Weyl semimetal TaAs
Authors: Zhang Cheng-Long , Wang C. M. , Yuan Zhujun , Xu Xitong , Wang Guangqiang , Lee Chi-Cheng , Pi Li , Xi Changying , Lin Hsin , Harrison Neil , Lu Hai-Zhou , Zhang Jinglei , Jia Shuang 
Published: March 2019

AbstractDetecting the spectroscopic signatures of relativistic quasiparticles in emergent topological materials is crucial for searching their potential applications. Magnetometry is a powerful tool for fathoming electrons in solids, by which a clear method for discerning relativistic quasiparticles has not yet been established. Adopting the probes of magnetic torque and parallel magnetization for the archetype Weyl semimetal TaAs in strong magnetic field, we observed a quasi-linear field dependent effective transverse magnetization and a non-saturating parallel magnetization when the system enters the quantum limit. Distinct from the saturating magnetic responses for non-relativistic quasiparticles, the non-saturating signals of TaAs in strong field is consistent with our newly developed magnetization calculation for a Weyl fermion system in an arbitrary angle. Our results establish a high-field thermodynamic method for detecting the magnetic response of relativistic quasiparticles in topological materials.
Deep convolutional neural networks for accurate somatic mutation detection
Authors: Sahraeian Sayed Mohammad Ebrahim , Liu Ruolin , Lau Bayo , Podesta Karl , Mohiyuddin Marghoob , Lam Hugo Y. K. 
Published: March 2019

AbstractAccurate detection of somatic mutations is still a challenge in cancer analysis. Here we present NeuSomatic, the first convolutional neural network approach for somatic mutation detection, which significantly outperforms previous methods on different sequencing platforms, sequencing strategies, and tumor purities. NeuSomatic summarizes sequence alignments into small matrices and incorporates more than a hundred features to capture mutation signals effectively. It can be used universally as a stand-alone somatic mutation detection method or with an ensemble of existing methods to achieve the highest accuracy.
Metagenomics and the development of viral water quality tools
Authors: Bibby Kyle , Crank Katherine , Greaves Justin , Li Xiang , Wu Zhenyu , Hamza Ibrahim A. , Stachler Elyse 
Published: March 2019

AbstractHuman exposure to pathogenic viruses in environmental waters results in a significant global disease burden. Current microbial water quality monitoring approaches, mainly based on fecal indicator bacteria, insufficiently capture human health impacts posed by pathogenic viruses in water. The emergence of the ‘microbiome era’ and high-throughput metagenome sequencing has led to the discovery of novel human-associated viruses, including both pathogenic and commensal viruses in the human microbiome. The discovery of novel human-associated viruses is often followed by their detection in wastewater, highlighting the great diversity of human-associated viruses potentially present in the water environment. Novel human-associated viruses provide a rich reservoir to develop viral water quality management tools with diverse applications, such as regulating wastewater reuse and monitoring agricultural and recreational waters. Here, we review the pathway from viral discovery to water quality monitoring tool, and highlight select human-associated viruses identified by metagenomics and subsequently detected in the water environment (namely Bocavirus, Cosavirus, CrAssphage, Klassevirus, and Pepper Mild Mottle Virus). We also discuss research needs to enable the application of recently discovered human-associated viruses in water quality monitoring, including investigating the geographic distribution, environmental fate, and viability of potential indicator viruses. Examples suggest that recently discovered human pathogens are likely to be less abundant in sewage, while other human-associated viruses (e.g., bacteriophages or viruses from food) are more abundant but less human-specific. The improved resolution of human-associated viral diversity enabled by metagenomic tools provides a significant opportunity for improved viral water quality management tools.
Approaching the potential of model-data comparisons of global land carbon storage
Authors: Wu Zhendong , Hugelius Gustaf , Luo Yiqi , Smith Benjamin , Xia Jianyang , Fensholt Rasmus , Lehsten Veiko , Ahlström Anders 
Published: March 2019

AbstractCarbon storage dynamics in vegetation and soil are determined by the balance of carbon influx and turnover. Estimates of these opposing fluxes differ markedly among different empirical datasets and models leading to uncertainty and divergent trends. To trace the origin of such discrepancies through time and across major biomes and climatic regions, we used a model-data fusion framework. The framework emulates carbon cycling and its component processes in a global dynamic ecosystem model, LPJ-GUESS, and preserves the model-simulated pools and fluxes in space and time. Thus, it allows us to replace simulated carbon influx and turnover with estimates derived from empirical data, bringing together the strength of the model in representing processes, with the richness of observational data informing the estimations. The resulting vegetation and soil carbon storage and global land carbon fluxes were compared to independent empirical datasets. Results show model-data agreement comparable to, or even better than, the agreement between independent empirical datasets. This suggests that only marginal improvement in land carbon cycle simulations can be gained from comparisons of models with current-generation datasets on vegetation and soil carbon. Consequently, we recommend that model skill should be assessed relative to reference data uncertainty in future model evaluation studies.
Quantized spin pump on helical edge states of a topological insulator
Authors: Wang Mei-Juan , Wang Jun , Liu Jun-Feng 
Published: March 2019

AbstractWe report a theoretical study of the quantized spin pump in a traditional quantum pump device that is based on the helical edge states of a quantum spin Hall insulator. By introducing two time-dependent magnetizations out of phase as the pumping parameters, we found that when the Fermi energy resides in the energy gap opened by magnetization, an integer number of charges or spins can be pumped out in a pumping cycle and ascribed to the possible topological interface state born in between the two pumping potentials. The quantized pump current can be fully spin-polarized, spin-unpolarized, or pure spin current while its direction can be abruptly reversed by some system parameters such as the pumping phase and local gate voltage. Our findings may shed light on generation of a quantized spin pump.
Non-conventional Ce:YAG nanostructures via urea complexes
Authors: Armetta Francesco , Saladino Maria Luisa , Giordano Cristina , Defilippi Chiara , Marciniak Łukasz , Hreniak Dariusz , Caponetti Eugenio 
Published: March 2019

AbstractCe:YAG nanostructures (Ce:YAG = Cerium in Yttrium Aluminium Garnet), easy to control and shape, have been prepared via templating approach using natural and synthetic materials (i.e. paper, cotton wool and glass wool) previously soaked with a gel-like metals precursor and then thermally treated to achieve the wished morphology. The final material, otherwise difficult to process, can be easily moulded, it is lightweight, portable and forms, at the nanoscale, homogeneous layers of interconnected but not agglomerated nanoparticles (15 ± 5 nm). Using the same synthetic route, called Urea-Glass-Route, but in absence of a template, extremely pure Ce:YAG nanoparticle (45 ± 5 nm) can be also prepared, highly crystalline and well-defined in size and shape. Both structural and optical properties of the final materials were investigated, showing high optical quality. The support allows the production of a multifunctional material with mouldable shape and potential lighting application for large structures combining the strength, chemical durability, fire resistance, and translucency of glass fibres. Last, but not least, the synthetic path also allows an easy scaling up of the process: the first, key step for practical application of nanosized rare-earth doped YAG on large scale.
Direct imaging of the recruitment and phosphorylation of S6K1 in the mTORC1 pathway in living cells
Authors: Ahmed Abdullah R. , Owens Raymond J. , Stubbs Christopher D. , Parker Anthony W. , Hitchman Richard , Yadav Rahul B. , Dumoux Maud , Hawes Chris , Botchway Stanley W. 
Published: March 2019

AbstractKnowledge of protein signalling pathways in the working cell is seen as a primary route to identifying and developing targeted medicines. In recent years there has been a growing awareness of the importance of the mTOR pathway, making it an attractive target for therapeutic intervention in several diseases. Within this pathway we have focused on S6 kinase 1 (S6K1), the downstream phosphorylation substrate of mTORC1, and specifically identify its juxtaposition with mTORC1. When S6K1 is co-expressed with raptor we show that S6K1 is translocated from the nucleus to the cytoplasm. By developing a novel biosensor we demonstrate in real-time, that phosphorylation and de-phosphorylation of S6K1 occurs mainly in the cytoplasm of living cells. Furthermore, we show that the scaffold protein raptor, that typically recruits mTOR substrates, is not always involved in S6K1 phosphorylation. Overall, we demonstrate how FRET-FLIM imaging technology can be used to show localisation of S6K1 phosphorylation in living cells and hence a key site of action of inhibitors targeting mTOR phosphorylation.
Prediction of future cognitive impairment among the community elderly: A machine-learning based approach
Authors: Na Kyoung-Sae 
Published: March 2019

AbstractThe early detection of cognitive impairment is a key issue among the elderly. Although neuroimaging, genetic, and cerebrospinal measurements show promising results, high costs and invasiveness hinder their widespread use. Predicting cognitive impairment using easy-to-collect variables by non-invasive methods for community-dwelling elderly is useful prior to conducting such a comprehensive evaluation. This study aimed to develop a machine learning-based predictive model for future cognitive impairment. A total of 3424 community elderly without cognitive impairment were included from the nationwide dataset. The gradient boosting machine (GBM) was exploited to predict cognitive impairment after 2 years. The GBM performance was good (sensitivity = 0.967; specificity = 0.825; and AUC = 0.921). This study demonstrated that a machine learning-based predictive model might be used to screen future cognitive impairment using variables, which are commonly collected in community health care institutions. With efforts of enhancing the predictive performance, such a machine learning-based approach can further contribute to the improvement of the cognitive function in community elderly.
Renal Damaging Effect Elicited by Bicalutamide Therapy Uncovered Multiple Action Mechanisms As Evidenced by the Cell Model
Authors: Peng Chiung Chi , Chen Chang-Yu , Chen Chang-Rong , Chen Chang-Jui , Shen Kun-Hung , Chen Kuan-Chou , Peng Robert Y. 
Published: March 2019

AbstractBicalutamide (Bic) is frequently used in androgen deprivation therapy (ADT) for treating prostate cancer. ADT-induced hypogonadism was reported to have the potential to lead to acute kidney injury (AKI). ADT was also shown to induce bladder fibrosis via induction of the transforming growth factor (TGF)-β level. We hypothesized that Bic can likely induce renal fibrosis. To understand this, a cell model was used to explore expressions of relevant profibrotic proteins. Results indicated that Bic initiated multiple apoptotic and fibrotic pathways, including androgen deprivation, downregulation of the androgen receptor → phosphatidylinositol-3-kinase → Akt pathway, upregulation of the extrinsic apoptotic pathway- tumor necrosis factor α →  nuclear factor κB → caspase-3, increased expressions of fibrosis-related proteins including platelet-derived growth factor β, fibronectin and collagen IV, and enhanced cell migration. The endoplasmic reticular stress pathway and smooth muscle actin were unaffected by Bic. Co-treatment with testosterone was shown to have an anti-apoptotic effect against Bic, suggesting a better outcome of Bic therapy if administered with an appropriate testosterone intervention. However, since Bic was found to inhibit the membrane transport and consumption rates of testosterone, a slightly larger dose of testosterone is recommended. In conclusion, these pathways can be considered to be pharmaceutically relevant targets for drug development in treating the adverse effects of Bic.
A unique and threatened deep water coral-bivalve biotope new to the Mediterranean Sea offshore the Naples megalopolis
Authors: Taviani Marco , Angeletti Lorenzo , Cardone Frine , Montagna Paolo , Danovaro Roberto 
Published: March 2019

AbstractThe Gulf of Naples is an example of the most beautiful and biodiverse marine regions of the Mediterranean Sea and of the most impacted areas in terms of industrial activities, large contaminated areas, resource exploitation, infrastructures at sea and maritime transportation. We conducted Remotely Operated Vehicle surveys in the Dohrn Canyon in the Tyrrhenian Sea at approximately 12 NM off Naples metropolitan area, and revealed a hotspot of deep-sea benthic biodiversity of sessile fauna at ca. 400 m depth. The hard bottoms are characterized by a high abundance of charismatic species, such as the habitat forming cold-water corals (CWC) Madrepora oculata, Lophelia pertusa, Desmophyllum dianthus in association with the large size bivalves Acesta excavata and Neopycnodonte zibrowii. This CWC-bivalve co-occurrence represents a novel biotope for the Mediterranean Sea, which coexists with the evidence of severe anthropogenic threats, such as illegal dumping and fishery malpractices that were visually documented during the survey. We recommend the adoption of specific protection measures to preserve these unique deep-sea assemblages showing the uncommon co-existence of such a number of deep-sea species in a single habitat.
NELFE-Dependent MYC Signature Identifies a Unique Cancer Subtype in Hepatocellular Carcinoma
Authors: Dang Hien , Pomyen Yotsawat , Martin Sean P. , Dominguez Dana A. , Yim Sun Young , Lee Ju-Seog , Budhu Anuradha , Shah Ashesh P. , Bodzin Adam S. , Wang Xin Wei 
Published: March 2019

AbstractThe MYC oncogene is dysregulated in approximately 30% of liver cancer. In an effort to exploit MYC as a therapeutic target, including in hepatocellular carcinoma (HCC), strategies have been developed on the basis of MYC amplification or gene translocation. Due to the failure of these strategies to provide accurate diagnostics and prognostic value, we have developed a Negative Elongation Factor E (NELFE)-Dependent MYC Target (NDMT) gene signature. This signature, which consists of genes regulated by MYC and NELFE, an RNA binding protein that enhances MYC-induced hepatocarcinogenesis, is predictive of NELFE/MYC-driven tumors that would otherwise not be identified by gene amplification or translocation alone. We demonstrate the utility of the NDMT gene signature to predict a unique subtype of HCC, which is associated with a poor prognosis in three independent cohorts encompassing diverse etiologies, demographics, and viral status. The application of gene signatures, such as the NDMT signature, offers patients access to personalized risk assessments, which may be utilized to direct future care.
Evidence of age-related improvement in the foraging efficiency of Adélie penguins
Authors: Lescroël Amélie , Ballard Grant , Massaro Melanie , Dugger Katie , Jennings Scott , Pollard Annie , Porzig Elizabeth , Schmidt Annie , Varsani Arvind , Grémillet David , Ainley David 
Published: March 2019

AbstractAge variation in reproductive performance is well-documented but the mechanisms underlying this variation remain unclear. Foraging efficiency is likely to be a key source of demographic variation as it determines the amount of energy that can be invested in fitness-related activities. Evidence of age-related changes in the foraging efficiency of adult seabirds is scarce and inconsistent. We investigated the effects of age on the foraging efficiency of breeding Adélie penguins, a relatively short-lived seabird species, in order to gain a broader perspective on the processes driving variation in ageing rates. We found support for a positive effect of age, either linear or levelling off at old ages, on both our proxies for daily catch rate and catch per unit effort. Across all age classes, males were more performant foragers than females. We found no strong evidence for differing ageing patterns between sexes or individual quality levels, and no evidence for senescence. We infer that continuous individual improvement could be responsible for a larger amount of the variation in foraging efficiency with age at our study site, compared with selective disappearance of underperforming phenotypes. The different results reported by other studies highlight the need to conduct longitudinal studies across a range of species in different environments.
Independent and combined effects of diethylhexyl phthalate and polychlorinated biphenyl 153 on sperm quality in the human and dog
Authors: Sumner Rebecca N. , Tomlinson Mathew , Craigon Jim , England Gary C. W. , Lea Richard G. 
Published: March 2019

AbstractA temporal decline in human and dog sperm quality is thought to reflect a common environmental aetiology. This may reflect direct effects of seminal chemicals on sperm function and quality. Here we report the effects of diethylhexyl phthalate (DEHP) and polychlorinated biphenyl 153 (PCB153) on DNA fragmentation and motility in human and dog sperm. Human and dog semen was collected from registered donors (n = 9) and from stud dogs (n = 11) and incubated with PCB153 and DEHP, independently and combined, at 0x, 2x, 10x and 100x dog testis concentrations. A total of 16 treatments reflected a 4 × 4 factorial experimental design. Although exposure to DEHP and/or PCB153 alone increased DNA fragmentation and decreased motility, the scale of dose-related effects varied with the presence and relative concentrations of each chemical (DEHP.PCB interaction for: DNA fragmentation; human p < 0.001, dog p < 0.001; Motility; human p < 0.001, dog p < 0.05). In both human and dog sperm, progressive motility negatively correlated with DNA fragmentation regardless of chemical presence (Human: P < 0.0001, r = −0.36; dog P < 0.0001, r = −0.29). We conclude that DEHP and PCB153, at known tissue concentrations, induce similar effects on human and dog sperm supporting the contention of the dog as a sentinel species for human exposure.
Merits and pitfalls of conventional and covalent docking in identifying new hydroxyl aryl aldehyde like compounds as human IRE1 inhibitors
Authors: Carlesso Antonio , Chintha Chetan , Gorman Adrienne M. , Samali Afshin , Eriksson Leif A. 
Published: March 2019

AbstractIRE1 is an endoplasmic reticulum (ER) bound transmembrane bifunctional kinase and endoribonuclease protein crucial for the unfolded protein response (UPR) signaling pathway. Upon ER stress, IRE1 homodimerizes, oligomerizes and autophosphorylates resulting in endoribonuclease activity responsible for excision of a 26 nucleotide intron from the X-box binding protein 1 (XBP1) mRNA. This unique splicing mechanism results in activation of the XBP1s transcription factor to specifically restore ER stress. Small molecules targeting the reactive lysine residue (Lys907) in IRE1α’s RNase domain have been shown to inhibit the cleavage of XBP1 mRNA. Crystal structures of murine IRE1 in complex with covalently bound hydroxyl aryl aldehyde (HAA) inhibitors show that these molecules form hydrophobic interactions with His910 and Phe889, a hydrogen bond with Tyr892 and an indispensable Schiff-base with Lys907. The availability of such data prompted interest in exploring structure-based drug design as a strategy to develop new covalently binding ligands. We extensively evaluated conventional and covalent docking for drug discovery targeting the catalytic site of the RNase domain. The results indicate that neither computational approach is fully successful in the current case, and we highlight herein the potential and limitations of the methods for the design of novel IRE1 RNase binders.
Corrosion mechanism and kinetics of Al-Zn coating deposited by arc thermal spraying process in saline solution at prolong exposure periods
Authors: Lee Han-Seung , Singh Jitendra Kumar , Ismail Mohamed A. , Bhattacharya Chinmoy , Seikh Asiful H. , Alharthi Nabeel , Hussain Raja Rizwan 
Published: March 2019

AbstractSteel structures significantly degrades owing to corrosion especially in coastal and industrial areas where significant amounts of aggressive ions are present. Therefore, anodic metals such as Al and Zn are used to protect steel. In the present study, we provide insights for the corrosion mechanism and kinetics of Al-Zn pseudo alloy coating deposited on mild steel plate via an arc thermal spraying process in 3.5 wt.% NaCl solution in terms of its improved corrosion resistance properties at prolonged exposure durations. Electrochemical studies including open circuit potential (OCP) and electrochemical impedance spectroscopy (EIS) on the deposited coating at longer exposure durations revealed enhanced corrosion resistance properties while the morphology of corrosion products through field emission-scanning electron microscopy (FE-SEM) indicated their compactness and adherence. Furthermore, atomic force microscopy (AFM) confirmed reduced roughness when compared with that of unexposed coating. Additionally, X-ray diffraction (XRD) and Raman spectroscopy results confirmed the formation of protective, adherent, and sparingly soluble Simonkolleite (Zn5(OH)8Cl2.H2O) after 55 d of exposure in 3.5 wt.% NaCl solution. A schematic is proposed that explains the corrosion process of Al–Zn pseudo alloy coating in 3.5 wt.% NaCl solution from the deposition of coating and initiation of corrosion to longer exposure durations.
Adsorption of Methylene Blue and Pb2+ by using acid-activated Posidonia oceanica waste
Authors: Elmorsi Randa R. , El-Wakeel Shaimaa T. , Shehab El-Dein Waleed A. , Lotfy Hesham R. , Rashwan Wafaa E. , Nagah Mohammed , Shaaban Seham A. , Sayed Ahmed Sohair A. , El-Sherif Iman Y. , Abou-El-Sherbini Khaled S. 
Published: March 2019

AbstractDead leaves of seagrassPosidonia oceanicawere activated by using one mol L−1acetic acid and used as an eco-adsorbent for the removal of methylene blue (MB) and Pb2+from aqueous solutions. The seagrass was characterized by chemical and physical measurements that confirmed the acid-activation of seagrass. The favourable conditions for MB and Pb2+adsorption onto the activated seagrass (SGa) were determined to be a pH range of 2–12 and ≥6, an adsorbent dosage of 3.0 and 0.5 g L−1, respectively, and a shaking time of 30 min, which are suitable for a wide range of wastewaters. The equilibrium data were analysed using the Langmuir, Freundlich and Dubinin-Raduskavich-Kaganer (DRK) adsorption isotherm models. The Freundlich and DRK models best describe the adsorption processes of MB and Pb2+, on SGawith capacities of 2681.9 and 631.13 mg g−1, respectively. The adsorption isotherm fitting and thermodynamic studies suggest that the adsorption mechanism of MB may combine electrostatic and physical multilayer adsorption processes, in which MB may be present as monomers as well as dimers and trimers which were confirmed from UV spectroscopy whereas Pb2+is chemically adsorbed onto SGa. The pseudo-2nd-order kinetic model was utilized to investigate the kinetics of adsorption processes. The removal process was successfully applied for MB-spiked brackish waste water from Manzala Lake, Egypt, with removal efficiencies of 91.5–99.9%.