bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nano sand filter with functionalized nanoparticles embedded in anodic aluminum oxide templates
Authors: Phuong NguyenThi , Andisetiawan Anugrah , Van Lam Do , Kim Jeong Hwan , Choi Doo-Sun , Whang Kyung-Hyun , Nham Jeasun , Lee Yun Jung , Yoo Yeong-Eun , Yoon Jae Sung 
Published: November 2016

AbstractSince the ancient Egyptians had used sand as filter media for water purification, its principle has been inherited through generations and it is still being used now in industries. The sand filter consists of sand literally, and the voids within the sand bed are the pores for filtration. Here we present a filtration principle using nanoparticles, so that the voids between the nanoparticles can be considered as effective pores in nanoscale dimension. Anodic aluminum oxide (AAO) membrane has been used as the working template, and the nanoparticles have been injected and embedded within the pores of the AAO template. Nanoparticles with multiple sizes have been used in order to obtain smaller voids. Moreover, the nanoparticles have been functionalized, or electrically charged, with arginine/phenylalanine (RF) peptide group. In this way, filtration performance for charged particles or molecules, such as methylene blue, has been enhanced. Consequently, this study is expected to provide a new principle for fabrication of nano voids, or nano pores, and for filtration in nanoscale dimension.
Negative Magnetoresistance in Amorphous Indium Oxide Wires
Authors: Mitra Sreemanta , Tewari Girish C , Mahalu Diana , Shahar Dan 
Published: November 2016

AbstractWe study magneto-transport properties of several amorphous Indium oxide nanowires of different widths. The wires show superconducting transition at zero magnetic field, but, there exist a finite resistance at the lowest temperature. The R(T) broadening was explained by available phase slip models. At low field, and far below the superconducting critical temperature, the wires with diameter equal to or less than 100 nm, show negative magnetoresistance (nMR). The magnitude of nMR and the crossover field are found to be dependent on both temperature and the cross-sectional area. We find that this intriguing behavior originates from the interplay between two field dependent contributions.
Dependence of phase configurations, microstructures and magnetic properties of iron-nickel (Fe-Ni) alloy nanoribbons on deoxidization temperature in hydrogen
Authors: Jing Panpan , Liu Mengting , Pu Yongping , Cui Yongfei , Wang Zhuo , Wang Jianbo , Liu Qingfang 
Published: November 2016

AbstractIron-nickel (Fe-Ni) alloy nanoribbons were reported for the first time by deoxidizing NiFe2O4 nanoribbons, which were synthesized through a handy route of electrospinning followed by air-annealing at 450 °C, in hydrogen (H2) at different temperatures. It was demonstrated that the phase configurations, microstructures and magnetic properties of the as-deoxidized samples closely depended upon the deoxidization temperature. The spinel NiFe2O4 ferrite of the precursor nanoribbons were firstly deoxidized into the body-centered cubic (bcc) Fe-Ni alloy and then transformed into the face-centered cubic (fcc) Fe-Ni alloy of the deoxidized samples with the temperature increasing. When the deoxidization temperature was in the range of 300 ~ 500 °C, although each sample possessed its respective morphology feature, all of them completely reserved the ribbon-like structures. When it was further increased to 600 °C, the nanoribbons were evolved completely into the fcc Fe-Ni alloy nanochains. Additionally, all samples exhibited typical ferromagnetism. The saturation magnetization (Ms) firstly increased, then decreased, and finally increased with increasing the deoxidization temperature, while the coercivity (Hc) decreased monotonously firstly and then basically stayed unchanged. The largest Ms (~145.7 emu·g−1) and the moderate Hc (~132 Oe) were obtained for the Fe-Ni alloy nanoribbons with a mixed configuration of bcc and fcc phases.
NR4A1 Knockdown Suppresses Seizure Activity by Regulating Surface Expression of NR2B
Authors: Zhang Yanke , Chen Guojun , Gao Baobing , Li Yunlin , Liang Shuli , Wang Xiaofei , Wang Xuefeng , Zhu Binglin 
Published: November 2016

AbstractNuclear receptor subfamily 4 group A member 1 (NR4A1), a downstream target of CREB that is a key regulator of epileptogenesis, has been implicated in a variety of biological processes and was previously identified as a seizure-associated molecule. However, the relationship between NR4A1 and epileptogenesis remains unclear. Here, we showed that NR4A1 protein was predominantly expressed in neurons and up-regulated in patients with epilepsy as well as pilocarpine-induced mouse epileptic models. NR4A1 knockdown by lentivirus transfection (lenti-shNR4A1) alleviated seizure severity and prolonged onset latency in mouse models. Moreover, reciprocal coimmunoprecipitation of NR4A1 and NR2B demonstrated their interaction. Furthermore, the expression of p-NR2B (Tyr1472) in epileptic mice and the expression of NR2B in the postsynaptic density (PSD) were significantly reduced in the lenti-shNR4A1 group, indicating that NR4A1 knockdown partly decreased surface NR2B by promoting NR2B internalization. These results are the first to indicate that the expression of NR4A1 in epileptic brain tissues may provide new insights into the molecular mechanisms underlying epilepsy.
One‐pot synthesis of net‐like silica materials with double mesoporous structure
Authors: Ma Yuanyuan , Deng Qingfang , Zhang Zhuanfang , Li Huanhuan , Jia Lihua 
Published: November 2016

A novel net‐like silica material with double mesoporous structure had been synthesised by one‐pot hydrothermal synthesis method. In the synthesis process, pluronic copolymer P123 (EO20PO70EO20) and non‐ionic surfactant OP‐10 were used as templates and potassium fluoride (KF) was chosen as the additive. A study was carried out by small‐angle X‐ray scattering, scanning electron microscopy and transmission electron microscopy for the physical properties of the resultant products. It was found that the net‐like silica materials exhibited a unique three‐dimensional morphology with the addition of KF and preserved mesoporous structure. Moreover, the samples had double mesopores of 3.6 and 6.5 nm by the result of the nitrogen adsorption isotherm.
Disorders of Consciousness: Practical Management in an Emergency Room
Authors: Damiani Daniel 
Published: November 2016

AbstractLowering of the level of consciousness is a very common presentation at the emergency room, often without any history that helps finding an etiology. This emergency requires quick empirical measures to reduce neuronal mortality, with additional protection against sequelae. According to the Advanced Cardiac Life Support (ACLS) guidelines, there are current emergency neurological support protocols, such as the Emergency Neurological Life Support (ENLS) created by the Neurocritical Care Society. The present paper shows how to approach unconscious patients, highlighting possible etiologies and proposed treatments.
Cytoskeleton dynamics control the first asymmetric cell division in
Arabidopsis
zygote
Authors: Kimata Yusuke , Higaki Takumi , Kawashima Tomokazu , Kurihara Daisuke , Sato Yoshikatsu , Yamada Tomomi , Hasezawa Seiichiro , Berger Frederic , Higashiyama Tetsuya , Ueda Minako 
Published: November 2016

Significance
In animals and plants, the zygote divides unequally, and the daughter cells inherit different developmental fates to form a proper embryo along the body axis. The cytological events leading to zygote polarization have remained unknown in flowering plants. Here, we report that the two essential components of the cytoskeleton, microtubules and actin filaments, are both disorganized on fertilization and then, arranged to form a transverse ring leading directional cell elongation and longitudinal arrays underlying polar nuclear migration, respectively. These results provide insights into the intracellular dynamics of zygote and the specific roles of cytoskeletons on zygote polarization in flowering plants.
Five‐a‐Day, Fruit and Vegetables Portions, and the Food Environment: The Italian Case
Authors: Bonanno Alessandro , Bimbo Francesco , Castellari Elena , Sckokai Paolo 
Published: November 2016

AbstractItaly has one of the largest per‐capita consumption rates of fruits and vegetables (FV) among European Union countries. However, the number of adult Italians consuming the recommended daily amounts of FV is declining, especially in regions where the food retail industry’s expansion is lagging. In this article we investigate the effect of the food environment on the likelihood of adult Italians consuming five or more daily portions of FV, and on the probability of consuming more portions of FV. We combine individual‐level data on adult Italians’ lifestyle with regional food retail structure measures. To correct for the endogeneity of the food environment, we use an identification strategy based on aggregate drivers of food stores’ location, and on the regional political climate affecting retail liberalization reforms. The results show that increased access affects positively the probability of consuming the daily‐recommended amounts of FV, as well as the probability of consuming more portions of FV. However, the role of the food environment is less marked for individuals declaring it to experience a hardship to access supermarkets.
Early Lymphocyte Recovery and Outcome in Osteosarcoma
Authors: Lee Lynn , Fei Lin , Pope Jennifer , Wagner Lars M. 
Published: November 2016

Background:
Early lymphocyte recovery following chemotherapy has been associated with improved outcome in many cancers, including in one small study of osteosarcoma patients.

Materials and Methods:
To confirm this finding, we retrospectively reviewed data from 53 patients with newly diagnosed osteosarcoma who had blood counts on day 14 (±1 d) following the first cycle of cisplatin and doxorubicin.

Results:
The median absolute lymphocyte count (ALC) 14 days after starting the first cycle of chemotherapy (ALC-14) was 1990 cells/μL (range: 600 to 6470). For 32 patients with an ALC-14≥1800 cells/μL, the 5-year progression-free survival (PFS) was 69%, compared with 33% for patients with an ALC-14 of <1800 cell/μL (P=0.036). In multivariable analysis of factors including age, sex, metastatic disease, and favorable histologic response to induction chemotherapy, ALC-14 was significantly associated with PFS (P=0.0081) and overall survival (P=0.0131). The use of ALC-14 appears to further stratify PFS and overall survival among patients when grouped by histologic response.

Conclusions:
We confirmed that early lymphocyte recovery was associated with outcome in pediatric osteosarcoma. Although presumably reflecting immune-mediated tumor control, the precise mechanism for this is unclear. Further study of peripheral blood lymphocyte subpopulations in prospectively treated patients is underway.
The Differential Diagnosis Between Natural Death and Homicide, an Everlasting Challenge for the Forensic Pathologist
Authors: di Luca Alessandro , de Matteis Valentino , Marcelli Antonio , Polacco Matteo , Pascali Vincenzo L. , Oliva Antonio 
Published: November 2016

Abstract
Most of the work performed by the forensic expert is to find proof for different plausible hypotheses that may be used in a trial to serve justice purposes when the “identity” of a case is already unveiled. Yet the previous phase of the investigation is also of great importance, and sometimes (like in the presented case), it represents the core element of the entire investigation. The appropriate determination of the differential diagnosis between a natural death and a death of forensic interest (ie, homicide) is the first and crucial step in the classification of a case. This article analyzes the case of the body of a man found lying on the border of a country road with his wrists tied up with rope and the resulting investigation performed by the medicolegal forensic expert. In the end, as more specific examinations where performed aimed to find the truth, the final conclusions excluded a violent death and confirmed that the cause of the death was an acute myocardial infarction.
Successful Treatment of Brachial Plexopathy Due to Herpes Zoster Infection With Intravenous Immunoglobulin
Authors: Sáenz-Farret Michel , Sandoval-Rodríguez Valeria , Paz-Navarro Claudia Esther , Zúñiga-Ramírez Carlos 
Published: November 2016

Objective
The aim of this study was to report the case of a male patient with Parkinson disease who developed brachial plexopathy (BP) due to varicella-zoster virus, which was successfully treated with human immunoglobulin.

Method
We report the case of a 75-year-old male subject with a diagnosis of Parkinson disease who came to our hospital complaining of pain, skin lesions, and strength loss in his right arm during the past 2 months. Physical examination revealed vesicular rash compatible with varicella-zoster virus lesions. Nerve conduction studies and magnetic resonance imaging of the brachial plexus showed inflammatory changes at that level. A trial with oral valacyclovir followed by intravenous methylprednisolone bolus was administered without further response. However, human intravenous immunoglobulin resulted in complete recovery of the symptoms.

Conclusions
Human immunoglobulin is effective in BP due to zoster infection and must be considered if standard treatment fails. To the best of our knowledge, this is the first report of BP associated to zoster infection successfully treated with intravenous immunoglobulin.
Zika and Chikungunya virus co-infection in a traveller returning from Colombia, 2016: virus isolation and genetic analysis
Authors: Cherabuddi Kartikeya , Iovine Nicole M. , Shah Kairav , White Sarah K. , Paisie Taylor , Salemi Marco , Morris Jr J. Glenn , Lednicky John A. 
Published: November 2016

Introduction:

Zika
virus (ZIKV) and Chikungunya
virus (CHIKV) can share the same mosquito vector, and co-infections by these viruses can occur in humans. While infections with these viruses share commonalities, CHIKV is unique in causing arthritis and arthralgias that may persist for a year or more. These infections are commonly diagnosed by RT–PCR-based methods during the acute phase of infection. Even with the high specificity and sensitivity characteristic of PCR, false negatives can occur, highlighting the need for additional diagnostic methods for confirmation.

Case presentation:
On her return to the USA, a traveller to Colombia, South America developed an illness consistent with Zika, Chikungunya and/or Dengue. RT-PCR of her samples was positive only for ZIKV. However, arthralgias persisted for months, raising concerns about co-infection with CHIKV or Mayaro viruses. Cell cultures inoculated with her original clinical samples demonstrated two types of cytopathic effects, and both ZIKV and CHIKV were identified in the supernatants. On phylogenetic analyses, both viruses were found to be related to strains found in Colombia.

Conclusion:
These findings highlight the need to consider CHIKV co-infection in patients with prolonged rheumatological symptoms after diagnosis with ZIKV, and the usefulness of cell culture as an amplification step for low-viremia blood and other samples.
The natural selection of metabolism explains curvature in fossil body mass evolution
Authors: Witting Lars 
Published: November 2016

AbstractThe natural selection of metabolism and mass can explain inter-specific allometries from prokaryotes to mammals (Witting 2017a), with exponents that depend on the selected metabolism and the spatial dimensionality (2D/3D) of intra-specific behaviour. The predicted 2D-exponent for total metabolism increases from 3/4 to 7/4 when the fraction of the inter-specific body mass variation that follows from primary variation in metabolism increases from zero to one.A 7/4 exponent for mammals has not been reported from inter-specific comparisons, but I detect the full range of allometries for evolution in the fossil record. There are no fossil data for allometric correlations between metabolism and mass, but I estimate life history allometries from the allometryfor the rate of evolutionin mass (w) in physical time (t).Theexponent describes the curvature of body mass evolution, with predicted values being: 3/2 (2D) for within niche evolution in small horses over 54 million years. 5/4 (2D) and 9/8 (3D) for across niche evolution of maximum mass in four mammalian clades. 3/4 (2D) for fast evolution in large horses, and maximum mass in trunked and terrestrial mammals. 1 for maximum mass across major life-forms during 3.5 billion years of evolution along a metabolic bound.
Rooting density differentiates wheat genotypes through Bayesian modeling
Authors: Wasson Anton P. , Chiu Grace S. , Zwart Alexander B. , Binns Timothy R. 
Published: November 2016

AbstractWheat pre-breeders use soil coring and core-break counts to phenotype root architecture traits, with data collected on rooting density for hundreds of genotypes in small increments of depth. The measured densities are both large datasets and highly variable even within the same genotype, hence, any rigorous, comprehensive statistical analysis of such complex field data would be technically challenging. Traditionally, most attributes of the field data are therefore discarded in favor of simple numerical summary descriptors which retain much of the high variability exhibited by the raw data. This poses practical challenges: although plant scientists have established that root traits do drive resource capture in crops, traits that are more randomly (rather than genetically) determined are difficult to breed for. In this paper we develop a Bayesian hierarchical nonlinear modeling approach that utilizes the complete field data for wheat genotypes to fit anidealizedrelative intensity function for the root distribution over depth. Our approach was used to determineheritability: how much of the variation between field samples was purely random versus being mechanistically driven by the plant genetics? Based on the genotypic intensity functions, the overall heritability estimate was 0.62 (95% Bayesian confidence interval was 0.52 to 0.71). Despite root count profiles that were statistically very noisy, our Bayesian analysis led to denoised profiles which exhibited rigorously discernible phenotypic traits. The profile-specific traits could be representative of a genotype and thus can be used as a quantitative tool to associate phenotypic traits with specific genotypes.
Scalable parameter estimation for genome-scale biochemical reaction networks
Authors: Fröhlich Fabian , Kaltenbacher Barbara , Theis Fabian J. , Hasenauer Jan 
Published: November 2016

AbstractMechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small-and medium-scale biological processes. While the same should in principle hold for large-and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large-and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics.Author SummaryIn this manuscript, we introduce a scalable method for parameter estimation for genome-scale biochemical reaction networks. Mechanistic models for genome-scale biochemical reaction networks describe the behavior of thousands of chemical species using thousands of parameters. Standard methods for parameter estimation are usually computationally intractable at these scales. Adjoint sensitivity based approaches have been suggested to have superior scalability but any rigorous evaluation is lacking. We implement a toolbox for adjoint sensitivity analysis for biochemical reaction network which also supports the import of SBML models. We show by means of a set of benchmark models that adjoint sensitivity based approaches unequivocally outperform standard approaches for large-scale models and that the achieved speedup increases with respect to both the number of parameters and the number of chemical species in the model. This demonstrates the applicability of adjoint sensitivity based approaches to parameter estimation for genome-scale mechanistic model. The MATLAB toolbox implementing the developed methods is available fromhttp://ICB-DCM.github.io/AMICI/.
Predicting gene expression level inE. colifrom mRNA sequence information
Authors: Zhao Linlin , Abedpour Nima , Blum Christopher , Kolkhof Petra , Beller Mathias , Kollmann Markus , Capriotti Emidio 
Published: November 2016

AbstractMotivationThe accurate characterization of the translational mechanism is crucial for enhancing our understanding of the relationship between genotype and phenotype. In particular, predicting the impact of the genetic variants on gene expression will allow to optimize specific pathways and functions for engineering new biological systems. In this context, the development of accurate methods for predicting translation efficiency from the nucleotide sequence is a key challenge in computational biology.MethodsIn this work we presentPGExpress, a binary classifier to discriminate between mRNA sequences with low and high translation efficiency inE.coli.PGExpressalgorithm takes as input 12 features corresponding to RNA folding and anti-Shine-Dalgarno hybridization free energies. The method was trained on a set of 1,772 sequence variants (WT-High) of 137 essentialE.coligenes. For each gene, we considered 13 sequence variants of the first 33 nucleotides encoding for the same amino acids followed by the superfolder GFP. Each gene variant is represented sequence blocks that include the Ribosome Binding Site (RBS), the first 33 nucleotides of the coding region (C33), the remaining part of the coding region (CC), and their combinations.ResultsOur logistic regression-based tool (PGExpress) was trained using a 20-fold gene-based cross-validation procedure on the WT-High dataset. In this testPGExpressachieved an overall accuracy of 74%, a Matthews correlation coefficient 0.49 and an Area Under the Receiver Operating Characteristic Curve (AUC) of 0.81. Tested on 3 sets of sequences with different Ribosome Binding Sites,PGExpressreaches similar AUC. Finally, we validated our method by performing in-house experiments on five newly generated mRNA sequence variants. The predictions of the expression level of the new variants are in agreement with our experimental results inE.coli.Availabilityhttp://folding.biofold.org/pgexpressContactmarkus.kollmann@hhu.de,emidio.capriotti@unibo.it