bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microscale disruption of microorganisms for parallelized process development
Authors: Walther Cornelia , Dürauer Astrid 
Published: June 2017

AbstractEscherichia coli, Saccharomyces cerevisiae, and Pichia pastoris are the standard platforms for biopharmaceutical production with 40% of all between 2010 to 2014 approved protein drugs produced in those microbial hosts. Typically, products overexpressed E. coli and S. cerevisiae remain in the cytosol or are secreted into the periplasm. Consequently, efficient cell disruption is essential for high product recovery during microbial production. Process development platforms at microscale are essential to shorten time to market. While high‐pressure homogenization is the industry standard for cell disruption at large scale this method is not practicable for experiments in microscale. This review describes microscale methods for cell disruption at scales as low as 200 µL. Strategies for automation, parallelization and miniaturization, as well as comparability of the results at this scale to high pressure homogenization are considered as those criteria decide which methods are most suited for scale down. Those aspects are discussed in detail for protein overexpression in E. coli and yeast but also the relevance for alternative products and host such as microalgae are taken into account. The authors conclude that bead milling is the best comparable microscale method to large scale high‐pressure homogenization and therefore the most suitable technique for automated process development of microbial hosts with the exception of pDNA production.
Vanadium Hydroxide Cluster Ions in the Gas Phase: Bond‐Forming Reactions of Doubly‐Charged Negative Ions by SO2‐Promoted V−O Activation
Authors: Troiani Anna , Rosi Marzio , Garzoli Stefania , Salvitti Chiara , de Petris Giulia 
Published: June 2017

AbstractThe gas‐phase reactivity of doubly‐charged vanadium hydroxides anions with SO2 has been studied by experimental and computational methods. The obtained results highlight the role of sulfur dioxide in promoting unprecedented bond‐forming reactions, which produce singly‐charged products by breaking the VxOy skeleton or a terminal V−O bond.
Water‐Mediated Structural Transformations of CuII 5‐Halonicotinates Coordination Networks with Distinct Mechanisms
Authors: Li Cheng‐Peng , Zhou Hang , Ju Yue , Du Miao 
Published: June 2017

AbstractCurrently, no unequivocal evidence is given for elucidation of “black box” during the structural transformations of dynamic crystalline materials. Here, three types of mechanisms are revealed for such transformations through X‐ray diffraction and optical microscopy; namely, single‐crystal to single‐crystal (SC–SC), as well as “core‐to‐core” and “core‐on‐shell” processes. As confirmed by time‐lapse optical microscopy, the latter two cases can be properly ascribed as partial recrystallization processes, while the former one is a continuous process with two different crystal lattices simultaneously maintained in one single crystal. Interestingly, these three distinct pathways can be exquisitely realized by changing only the halogen substituent (from ‐F, ‐Cl, to ‐Br) of the organic ligands in the coordination supramolecular systems.
A Highly Sensitive Enzymatic Catalysis System for Trace Detection of Arsenic in Water
Authors: Liu Yuanli , Yu Chuanbai , Cao Zhixin , Shvarts Daniel , Trogler William C. 
Published: June 2017

AbstractArsenic (As) is an extremely toxic element that exists in the environment in different chemical forms. The detection of arsenic in potable water remains a challenging task. This study presents a highly sensitive enzymatic catalysis system for trace sensing of inorganic arsenic in water. This is the first enzyme‐catalyzed fluorescence assay capable of detecting arsenic at concentrations below the allowable level adopted by the World Health Organization (10 ppb in drinking water). The enzyme catalytically produces fluorescent NADH in the presence of arsenate, which enables facile detection of arsenate at concentrations in the 0–200 ppb range. Calibration curves made at a set time interval allow accurate determination of unknown arsenic samples. This method holds potential for interfacing with automated analytical sampling systems to allow arsenic determinations in environmental health applications.
Piecewise holistic autotuning of parallel programs with CERE
Authors: Popov Mihail , Akel Chadi , Chatelain Yohan , Jalby William , de Oliveira Castro Pablo 
Published: June 2017

SummaryCurrent architecture complexity requires fine tuning of compiler and runtime parameters to achieve best performance. Autotuning substantially improves default parameters in many scenarios, but it is a costly process requiring long iterative evaluations. We propose an automatic piecewise autotuner based on CERE (Codelet Extractor and REplayer). CERE decomposes applications into small pieces called codelets: Each codelet maps to a loop or to an OpenMP parallel region and can be replayed as a standalone program. Codelet autotuning achieves better speedups at a lower tuning cost. By grouping codelet invocations with the same performance behavior, CERE reduces the number of loops or OpenMP regions to be evaluated. Moreover, unlike whole‐program tuning, CERE customizes the set of best parameters for each specific OpenMP region or loop. We demonstrate the CERE tuning of compiler optimizations, number of threads, thread affinity, and scheduling policy on both nonuniform memory access and heterogeneous architectures. Over the NAS benchmarks, we achieve an average speedup of 1.08× after tuning. Tuning a codelet is 13× cheaper than whole‐program evaluation and predicts the tuning impact with a 94.7% accuracy. Similarly, exploring thread configurations and scheduling policies for a Black‐Scholes solver on an heterogeneous big.LITTLE architecture is over 40× faster using CERE.
A new volunteer computing model for data‐intensive applications
Authors: Alonso‐Monsalve Saúl , García‐Carballeira Félix , Calderón Alejandro 
Published: June 2017

SummaryVolunteer computing is a type of distributed computing in which ordinary people donate computing resources to scientific projects. BOINC is the main middleware system for this type of distributed computing. The aim of volunteer computing is that organizations be able to attain large computing power thanks to the participation of volunteer clients instead of a high investment in infrastructure. There are projects, like the ATLAS@Home project, in which the number of running jobs has reached a plateau, due to a high load on data servers caused by file transfer. This is why we have designed an alternative, using the same BOINC infrastructure, in order to improve the performance of BOINC projects that have reached their limit due to the I/O bottleneck in data servers. This alternative involves having a percentage of the volunteer clients running as data servers, called data volunteers, that improve the performance of the system by reducing the load on data servers. In addition, our solution takes advantage of data locality, leveraging the low network latencies of closer machines. This paper describes our alternative in detail and shows the performance of the solution, applied to 3 different BOINC projects, using a simulator of our own, ComBoS.
Semantic keyword searchable proxy re‐encryption for postquantum secure cloud storage
Authors: Yang Yang , Zheng Xianghan , Chang Victor , Tang Chunming 
Published: June 2017

SummaryWith the advent of cloud computing, more and more consumers prefer to use the cloud services with the pay‐as‐you‐consume mode. The cloud storage brings about great convenience to users, who store data in cloud and access to it using the smart devices anytime and anywhere. Consumers' information should be encrypted to guarantee the data privacy. Flexible searching on ciphertext is a critical challenge to be solved for effective data utilization. In this paper, we propose a novel semantic keyword searchable proxy re‐encryption scheme for secure cloud storage. A highlight of this work is that the scheme is quantum attack resistant, while most of the available searchable encryption schemes are not. It supports not only exact keyword search but also synonym keyword search. Moreover, the data owner is capable to delegate his search right to another user using the proxy re‐encryption mechanism. In the generation process of re‐encryption key, the delegator and delegatee do not need to be interactive with each other. The scheme is also collusion resistant. Under the learning with errors hardness problem, this scheme is proved secure in standard model.
Research on network programming language and policy conflicts for SDN
Authors: He Bohan , Dong Ligang , Xu Tijie , Fei Shuocheng , Zhang Huafei , Wang Weiming 
Published: June 2017

SummaryThrough network programmability, software defined network can simplify network control and management. Since the current software defined network southbound interface level is low and programming situation is complex, it requires a high‐level abstract programming language to simplify programming. First, this paper improves the NetCore programming language to generate NetCore‐M language, so that it can support deployment of multipolicies combination including packet drop action. This paper describes in detail the syntax, semanteme, and implementation of NetCore‐M language forwarding policy service. Secondly, this paper describes the network policy conflict systematically. Finally, this paper shows that the modified multipolicies combination algorithm can effectively detect policies conflicts based on the implementation of the Pyretic project.
Defect‐Based Modulation of Optoelectronic Properties for Biofunctionalized Hexagonal Boron Nitride Nanosheets
Authors: Shakourian‐Fard Mehdi , Heydari Hadiseh , Kamath Ganesh 
Published: June 2017

AbstractDefect engineering potentially allows for dramatic tuning of the optoelectronic properties of two‐dimensional materials. With the help of DFT calculations, a systematic study of DNA nucleobases adsorbed on hexagonal boron‐nitride nanoflakes (h‐BNNFs) with boron (VB) and nitrogen (VN) monovacancies is presented. The presence of VNand VBdefects increases the binding strength of nucleobases by 9 and 34 kcal mol−1, respectively (h‐BNNF‐VB>h‐BNNF‐VN>h‐BNNF). A more negative electrostatic potential at the VBsite makes the h‐BNNF‐VBsurface more reactive than that of h‐BNNF‐VN, enabling H‐bonding interactions with nucleobases. This binding energy difference affects the recovery time—a significant factor for developing DNA biosensors—of the surfaces in the order h‐BNNF‐VB>h‐BNNF‐VN>h‐BNNF. The presence of VBand VNdefect sites increases the electrical conductivity of the h‐BNNF surface, VNdefects being more favorable than VBsites. The blueshift of absorption peaks of the h‐BNNF‐VB–nucleobase complexes, in contrast to the redshift observed for h‐BNNF‐VN–nucleobase complexes, is attributed to their observed differences in binding energies, the HOMO–LUMO energy gap and other optoelectronic properties. Time‐dependent DFT calculations reveal that the monovacant boron‐nitride‐sheet–nucleobase composites absorb visible light in the range 300–800 nm, thus making them suitable for light‐emitting devices and sensing nucleobases in the visible region.
Aeolian sediment fingerprinting using a Bayesian mixing model
Authors: Gholami Hamid , Telfer Matt W. , Blake William H. , Fathabadi Abolhassan 
Published: June 2017

AbstractIdentifying sand provenance in depositional aeolian environments (e.g. dunefields) can elucidate sediment pathways and fluxes, and inform potential land management strategies where windblown sand and dust is a hazard to health and infrastructure. However, the complexity of these pathways typically makes this a challenging proposition, and uncertainties on the composition of mixed‐source sediments are often not reported. This study demonstrates that a quantitative fingerprinting method within the Bayesian Markov Chain Monte Carlo (MCMC) framework offers great potential for exploring the provenance and uncertainties associated with aeolian sands.Eight samples were taken from dunes of the small (~58 km2) Ashkzar erg, central Iran, and 49 from three distinct potential sediment sources in the surrounding area. These were analyzed for 61 tracers including 53 geochemical elements (trace, major and rare earth elements (REE)) and eight REE ratios. Kruskal–Wallis H‐tests and stepwise discriminant function analysis (DFA) allowed the identification of an optimum composite fingerprint based on six tracers (Rb, Sr,87Sr, (La/Yb)n, Ga and δCe), and a Bayesian mixing model was applied to derive the source apportionment estimates within an uncertainty framework.There is substantial variation in the uncertainties in the fingerprinting results, with some samples yielding clear discrimination of components, and some with less clear fingerprints. Quaternary terraces and fans contribute the largest component to the dunes, but they are also the most extensive surrounding unit; clay flats and marls, however, contribute out of proportion to their small outcrop extent. The successful application of these methods to aeolian sediment deposits demonstrates their potential for providing quantitative estimates of aeolian sediment provenances in other mixed‐source arid settings, and may prove especially beneficial where sediment is derived from multiple sources, or where other methods of provenance (e.g. detrital zircon U–Pb dating) are not possible due to mineralogical constraints. Copyright © 2017 John Wiley & Sons, Ltd.
Medaka extended one-generation reproduction test evaluating 4-nonylphenol
Authors: Watanabe Haruna , Horie Yoshifumi , Takanobu Hitomi , Koshio Masaaki , Flynn Kevin , Iguchi Taisen , Tatarazako Norihisa 
Published: June 2017

Abstract

The medaka extended one-generation test (MEOGRT) was developed as a multigenerational toxicity test for chemicals, particularly endocrine-disrupting chemicals. Briefly, 3 generations of Japanese medaka (Oryzias latipes) are exposed to a chemical over a 20-wk period: 3 wk in the parental generation (F0), 15 wk in the first generation (F1), and 2 wk in the second generation (F2). The present study reports the first MEOGRT results concerning branched isomer mixtures of 4-nonylphenol (NP). Adult F0 medaka exposed to NP at 5 actual concentrations (1.27, 2.95, 9.81, 27.8, 89.4 µg/L) were unaffected in terms of reproduction, although vitellogenin in the male liver was increased dose-dependently at concentration of 2.95 µg/L and higher. In F1, in contrast, total egg (fecundity), fertile egg, and fertility decreased as NP increased; lowest-observed-effect concentrations (LOECs) for total egg, fertile egg, and fertility were 1.27, 1.27, 27.8 µg/L, respectively. In F1, but not in F0, secondary sex characteristics (i.e., anal fin papillae in males) were suppressed at 27.8 µg/L NP. Vitellogenin induction in adult male fish was slightly weaker in F1 than it was in F0, however. Gonadal sex abnormality and sex reversal occurred at 27.8 and 89.4 µg/L NP in F1 subadults. At 89.4 µg/L NP, all genotypic F1 males in breeding pairs had female phenotype, and some even demonstrated spawning. Concentrations of NP lower than 89.4 µg/L did not affect F2 survival or hatching. The highest detected NP level in environmental freshwater in Japan was approximately a half of the LOEC (1.27 µg/L for F1 fecundity); in other countries, however, environmental concentrations above the LOEC are reported, suggesting that NP may be affecting fish populations. Environ Toxicol Chem 2017;36:3254–3266. © 2017 SETAC
Sensory response in host and engrafted astrocytes of adult brain in Vivo
Authors: Zhang Kuan , Chen Xiaowei 
Published: June 2017

AbstractRapid advances in Ca2+ imaging techniques enable us to simultaneously monitor the activities of hundreds of astrocytes in the intact brain, thus providing a powerful tool for understanding the functions of both host and engrafted astrocytes in sensory processing in vivo. These techniques include both improved Ca2+ indicators and advanced optical recording methods. Astrocytes in multiple cortical and sub‐cortical areas are able to respond to the corresponding sensory modalities. These sensory stimuli produce astrocytic Ca2+ responses through different cellular mechanisms. In addition, it has been suggested that astrocytic gene deficiencies in various sensory systems cause impairments in sensory circuits and cognition. Therefore, glial transplantation would be a potentially interesting approach for the cell‐based therapy for glia‐related disorders. There are multiple cell sources for glial transplantation, including neural stem cells, glial progenitors, and pluripotent stem cells. Both in vitro and in vivo studies have shown that engrafted astrocytes derived from these cell sources are capable of responding to sensory stimulation by elevating the intracellular Ca2+ concentration. These results indicate that engrafted astrocytes not only morphologically but also functionally integrate into the host neural network. Until now, many animal studies have proven that glial transplantation would be a good choice for treating multiple glial disorders. Together, these studies on the sensory responses of host and engrafted astrocytes have provided us a novel perspective in both neuron‐glia circuit functions and future treatment strategies for glial disorders.
Profile, effects, and toxicity of novel psychoactive substances: A systematic review of quantitative studies
Authors: Assi Sulaf , Gulyamova Nargilya , Ibrahim Kinda , Kneller Paul , Osselton David 
Published: June 2017

ObjectiveTo investigate the profile, effects, and toxicity of novel psychoactive substances (NPS).MethodsA systematic literature review was conducted between May 2015 and February 2016 and included 19 databases. Search terms included “novel psychoactive substance(s),” “effect(s),” and “toxicity” and their synonyms. Studies included were those from any country, in any language, and between January 2007 and April 2015. Studies published before 2007 and those regarding the synthesis of NPS were excluded. Data were extracted by evaluating the titles, abstract, and full text, respectively. Consequently, the extraction yielded 20 studies.ResultsForty‐three NPS derivatives of 8 main pharmacological classes were identified. NPS were mostly used among young adults and adults within the age range of 16–64 years old. Cathinones and synthetic cannabinoids were the most prevalent among the aforementioned classes. The main desired effects of NPS use were empathy and increased ability to socialise. Reported toxicity associated with the use of NPS included cardiovascular, neurological, and psychoactive adverse reactions.ConclusionsDespite the unique subjective effects associated with the use of NPS, harmful effects could be severe and/or lethal. Therefore, there is a need to develop research in the area of NPS and promote awareness among healthcare professionals.
A phase II trial evaluating the feasibility of adding bevacizumab to standard osteosarcoma therapy
Authors: Navid Fariba , Santana Victor M. , Neel Michael , McCarville M. Beth , Shulkin Barry L. , Wu Jianrong , Billups Catherine A. , Mao Shenghua , Daryani Vinay M. , Stewart Clinton F. , Kunkel Michelle , Smith Wendene , Ward Deborah , Pappo Alberto S. , Bahrami Armita , Loeb David M. , Reikes Willert Jennifer , Rao Bhaskar N. , Daw Najat C. 
Published: June 2017

Increased vascular endothelial growth factor (VEGF) expression in osteosarcoma correlates with a poor outcome. We conducted a phase II trial to evaluate the feasibility and efficacy of combining bevacizumab, a monoclonal antibody against VEGF, with methotrexate, doxorubicin and cisplatin (MAP) in patients with localized osteosarcoma. Eligible patients received two courses of MAP chemotherapy before definitive surgery at week 10. Bevacizumab (15 mg/kg) was administered 3 days before starting chemotherapy then on day 1 of weeks 3 and 5 of chemotherapy. After surgery, patients received MAP for a total of 29 weeks; bevacizumab was added every 2 or 3 weeks on day 1 of chemotherapy at least 5 weeks after surgery. Group sequential monitoring rules were used to monitor for unacceptable bevacizumab‐related targeted toxicity (grade 4 hypertension, proteinuria or bleeding, grade 3 or 4 thrombosis/embolism, and grade 2–4 major wound complications). Thirty‐one patients (median age 12.8 years) with localized osteosarcoma were enrolled. No unacceptable targeted toxicities were observed except for wound complications (9 minor and 6 major), which occurred in 15 patients; none required removal of prosthetic hardware or amputation. The estimated 4‐year event‐free survival (EFS) rate and overall survival rate were 57.5 ± 10.0% and 83.4 ± 7.8%, respectively. Eight (28%) of 29 evaluable patients had good histologic response (<5% viable tumor) to preoperative chemotherapy. The addition of bevacizumab to MAP for localized osteosarcoma is feasible but frequent wound complications are encountered. The observed histologic response and EFS do not support further evaluation of bevacizumab in osteosarcoma.
Mild metabolic perturbations alter succinylation of mitochondrial proteins
Authors: Chen Huanlian , Xu Hui , Potash Samuel , Starkov Anatoly , Belousov Vsevolod V. , Bilan Dmitry S. , Denton Travis T. , Gibson Gary E. 
Published: June 2017

AbstractSuccinylation of proteins is widespread, modifies both the charge and size of the molecules, and can alter their function. For example, liver mitochondrial proteins have 1,190 unique succinylation sites representing multiple metabolic pathways. Succinylation is sensitive to both increases and decreases of the NAD+‐dependent desuccinylase, SIRT5. Although the succinyl group for succinylation is derived from metabolism, the effects of systematic variation of metabolism on mitochondrial succinylation are not known. Changes in succinylation of mitochondrial proteins following variations in metabolism were compared against the mitochondrial redox state as estimated by the mitochondrial NAD+/NADH ratio using fluorescent probes. The ratio was decreased by reduced glycolysis and/or glutathione depletion (iodoacetic acid; 2‐deoxyglucose), depressed tricarboxylic acid cycle activity (carboxyethyl ester of succinyl phosphonate), and impairment of electron transport (antimycin) or ATP synthase (oligomycin), while uncouplers of oxidative phosphorylation (carbonyl cyanide m‐chlorophenyl hydrazine or tyrphostin) increased the NAD+/NADH ratio. All of the conditions decreased succinylation. In contrast, reducing the oxygen from 20% to 2.4% increased succinylation. The results demonstrate that succinylation varies with metabolic states, is not correlated to the mitochondrial NAD+/NADH ratio, and may help coordinate the response to metabolic challenge.
Detection of weekly cycles in atmospheric data
Authors: Jolliffe I. T. 
Published: June 2017

ABSTRACTThere is considerable interest in whether weekly cycles are present in certain types of atmospheric and hydrologic data. Seven days is not a natural period for cyclic behaviour, but rather a human construct. Hence the presence of weekly cycles can help to confirm the presence and nature of anthropogenic climate change. Several statistical tests have been used to investigate the presence of such cycles. In this short note, a test previously used for ‘flatness’ of rank histograms in ensemble forecasting is shown to be useful for this task for certain types of data, with some advantages compared with existing techniques. Some disadvantages and extensions are also described.