bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a soft‐sensor based on multi‐wavelength fluorescence spectroscopy and a dynamic metabolic model for monitoring mammalian cell cultures
Authors: Ohadi Kaveh , Legge Raymond L. , Budman Hector M. 
Published: July 2014

ABSTRACTA soft‐sensor based on an Extended Kalman Filter (EKF) that combines data obtained using a fluorescence‐based soft‐sensor with a dynamic mechanistic model, was investigated as a tool for continuous monitoring of a Chinese hamster ovary (CHO) cell cultivation process. A standalone fluorescence based soft‐sensor, which uses a combination of an empirical multivariate statistical model and measured spectra, was designed for predicting key culture variables including viable and dead cells, recombinant protein, glucose, and ammonia concentrations. The standalone fluorescence sensor was then combined with a dynamic mechanistic model within an EKF framework, for improving the prediction accuracy and generating predictions in‐between sampling instances. The dynamic model used for the EKF framework was based on a structured metabolic flux analysis and mass balances. In order to calibrate the fluorescence‐based empirical model and the dynamic mechanistic model, cells were grown in batch mode with different initial glucose and glutamine concentrations. To mitigate the uncertainty associated with the model structure and parameters, non‐stationary disturbances were accounted for in the EKF by parameter‐adaptation. It was demonstrated that the implementation of the EKF along with the dynamic model could improve the accuracy of the fluorescence‐based predictions at the sampling instances. Additionally, it was shown that the major advantage of the EKF‐based soft‐sensor, compared to the standalone fluorescence‐based counterpart, was its capability to track the temporal evolution of key process variables between measurement instances obtained by the fluorescence‐based soft‐sensor. This is crucial for designing control strategies of CHO cell cultures with the aim of guaranteeing product quality. Biotechnol. Bioeng. 2015;112: 197–208. © 2014 Wiley Periodicals, Inc.
A novel UPLC‐MS/MS method for sensitive quantitation of boldine in plasma, a potential anti‐inflammatory agent: application to a pharmacokinetic study in rats
Authors: Zeng Rong‐Jie , Li Yu , Chen Jian‐Zhong , Chou Gui‐Xin , Gao Yu , Shao Jing‐Wei , Jia Lee , Wu Sheng‐Dong , Wu Shui‐Sheng 
Published: July 2014

AbstractBoldine is a potential anti‐inflammatory agent found in several different plants. Published bioanalytical methods using HPLC with ultraviolet and fluorescent detection lacked enough sensitivity and required tedious sample preparation procedures. Herein, we describe the development of a novel ultra‐high performance LC with MS/MS for determination of boldine in plasma. Boldine in plasma was recovered by liquid–liquid extraction using 1 mL of methyl tert‐butyl ether. Chromatographic separation was performed on a C18 column at 45°C, with a gradient elution consisting of acetonitrile and water containing 0.1% (v/v) formic acid at a flow rate of 0.3 mL/min. The detection was performed on an electrospray triple‐quadrupole MS/MS by positive ion multiple reaction monitoring mode. Good linearity (r2 > 0.9926) was achieved in a concentration range of 2.555–2555 ng/mL with a lower limit of quantification of 2.555 ng/mL for boldine. The intra‐ and inter‐day precisions of the assay were 1.2–6.0 and 1.8–7.4% relative standard deviation with an accuracy of −6.0–8.0% relative error. This newly developed method was successfully applied to a single low‐dose pharmacokinetic study in rats and was demonstrated to be simpler and more sensitive than the published methods, allowing boldine quantification in reduced plasma volume. Copyright © 2014 John Wiley & Sons, Ltd.
HPV‐positive oropharyngeal squamous cell carcinoma is associated with TIMP3 and CADM1 promoter hypermethylation
Authors: van Kempen Pauline M. W. , van Bockel Liselotte , Braunius Weibel W. , Moelans Cathy B. , van Olst Marina , de Jong Rick , Stegeman Inge , van Diest Paul J. , Grolman Wilko , Willems Stefan M. 
Published: July 2014

AbstractOropharyngeal squamous cell carcinoma (OPSCC) is associated with human papillomavirus (HPV) in a proportion of tumors. HPV‐positive OPSCC is considered a distinct molecular entity with a prognostic advantage compared to HPV‐negative cases. Silencing of cancer‐related genes by DNA promoter hypermethylation may play an important role in the development of OPSCC. Hence, we examined promoter methylation status in 24 common tumor suppressor genes in a group of 200 OPSCCs to determine differentially methylated genes in HPV‐positive versus HPV‐negative primary OPSCC. Methylation status was correlated with HPV status, clinical features, and patient survival using multivariate methods. Additionally, methylation status of 16 cervical squamous cell carcinomas (SCC) was compared with HPV‐positive OPSCC. Using methylation‐specific probe amplification, HPV‐positive OPSCC showed a significantly higher cumulative methylation index (CMI) compared to HPV‐negative OPSCC (P=0.008). For the genes CDH13, DAPK1, and RARB, both HPV‐positive and HPV‐negative OPSCC showed promoter hypermethylation in at least 20% of the tumors. HPV status was found to be an independent predictor of promoter hypermethylation of CADM1 (P < 0.001), CHFR (P = 0.027), and TIMP3 (P < 0.001). CADM1 and CHFR showed similar methylation patterns in OPSCC and cervical SCC, but TIMP3 showed no methylation in cervical SCC in contrast to OPSCC. Methylation status of neither individual gene nor CMI was associated with survival. These results suggest that HPV‐positive tumors are to a greater extent driven by promotor hypermethylation in these tumor suppressor genes. Especially CADM1 and TIMP3 are significantly more frequently hypermethylated in HPV‐positive OPSCC and CHFR in HPV‐negative tumors.
Using ecological momentary assessment to examine interpersonal and affective predictors of loss of control eating in adolescent girls
Authors: Ranzenhofer Lisa M. , Engel Scott G. , Crosby Ross D. , Anderson Micheline , Vannucci Anna , Cohen L. Adelyn , Cassidy Omni , Tanofsky‐Kraff Marian 
Published: July 2014

ABSTRACTObjectivePediatric loss of control (LOC) eating is predictive of partial‐ and full‐syndrome binge eating disorder. The interpersonal model proposes that LOC eating is used to cope with negative mood states resulting from interpersonal distress, possibly on a momentary level. We therefore examined temporal associations between interpersonal problems, negative affect, and LOC eating among overweight adolescent girls using ecological momentary assessment (EMA).MethodThirty overweight and obese (≥85th body mass index (BMI) percentile; BMI: M = 36.13, SD = 7.49 kg/m2) adolescent females (Age: M = 14.92, SD = 1.54 y; 60.0% African American) who reported at least two LOC episodes in the past month completed self‐report momentary ratings of interpersonal problems, state affect, and LOC eating for 2 weeks. A series of 2‐level multilevel models with centering within subjects was conducted.ResultsBetween‐ and within‐subjects interpersonal problems (p's < .05), but not between‐ (p = .12) or within‐ (p = .32) subjects negative affect predicted momentary LOC eating. At the between‐subjects level, interpersonal problems significantly predicted increases in negative affect (p < 001).DiscussionNaturalistic data lend support to the predictive value of interpersonal problems for LOC eating among adolescents. Interventions targeting interpersonal factors on a momentary basis may be useful during this developmental stage. © 2014 Wiley Periodicals, Inc. (Int J Eat Disord 2014; 47:748–757)
The relationship of leaf photosynthetic traits – Vcmax and Jmax – to leaf nitrogen, leaf phosphorus, and specific leaf area: a meta‐analysis and modeling study
Authors: Walker Anthony P. , Beckerman Andrew P. , Gu Lianhong , Kattge Jens , Cernusak Lucas A. , Domingues Tomas F. , Scales Joanna C. , Wohlfahrt Georg , Wullschleger Stan D. , Woodward F. Ian 
Published: July 2014

AbstractGreat uncertainty exists in the global exchange of carbon between the atmosphere and the terrestrial biosphere. An important source of this uncertainty lies in the dependency of photosynthesis on the maximum rate of carboxylation (Vcmax) and the maximum rate of electron transport (Jmax). Understanding and making accurate prediction of C fluxes thus requires accurate characterization of these rates and their relationship with plant nutrient status over large geographic scales. Plant nutrient status is indicated by the traits: leaf nitrogen (N), leaf phosphorus (P), and specific leaf area (SLA). Correlations between Vcmax and Jmax and leaf nitrogen (N) are typically derived from local to global scales, while correlations with leaf phosphorus (P) and specific leaf area (SLA) have typically been derived at a local scale. Thus, there is no global‐scale relationship between Vcmax and Jmax and P or SLA limiting the ability of global‐scale carbon flux models do not account for P or SLA. We gathered published data from 24 studies to reveal global relationships of Vcmax and Jmax with leaf N, P, and SLA. Vcmax was strongly related to leaf N, and increasing leaf P substantially increased the sensitivity of Vcmax to leaf N. Jmax was strongly related to Vcmax, and neither leaf N, P, or SLA had a substantial impact on the relationship. Although more data are needed to expand the applicability of the relationship, we show leaf P is a globally important determinant of photosynthetic rates. In a model of photosynthesis, we showed that at high leaf N (3 gm−2), increasing leaf P from 0.05 to 0.22 gm−2 nearly doubled assimilation rates. Finally, we show that plants may employ a conservative strategy of Jmax to Vcmax coordination that restricts photoinhibition when carboxylation is limiting at the expense of maximizing photosynthetic rates when light is limiting.
Calcium signaling in cilia and ciliary-mediated intracellular calcium signaling: Are they independent or coordinated molecular events?
Authors: Masyuk Anatoliy I. , Gradilone Sergio A. , LaRusso Nicholas F. 
Published: July 2014

Abstract

Primary cilia are solitary, non-motile extensions of the centriole found on nearly all nucleated eukaryotic cells between cell divisions. Only ˜200-300 nm in diameter and a few micrometers long, they are separated from the cytoplasm by the ciliary neck and basal body. Often called sensory cilia, they are thought to receive chemical and mechanical stimuli and initiate specific cellular signal transduction pathways. When activated by a ligand, hedgehog pathway proteins, such as GLI2 and smoothened (SMO), translocate from the cell into the cilium. Mutations in primary ciliary proteins are associated with severe developmental defects. The ionic conditions, permeability of the primary cilia membrane, and effectiveness of the diffusion barriers between the cilia and cell body are unknown. Here we show that cilia are a unique calcium compartment regulated by a heteromeric TRP channel, PKD1L1-PKD2L1, in mice and humans. In contrast to the hypothesis that polycystin (PKD) channels initiate changes in ciliary calcium that are conducted into the cytoplasm, we show that changes in ciliary calcium concentration occur without substantially altering global cytoplasmic calcium. PKD1L1-PKD2L1 acts as a ciliary calcium channel controlling ciliary calcium concentration and thereby modifying SMO-activated GLI2 translocation and GLI1 expression.

Abstract

A primary cilium is a solitary, slender, non-motile protuberance of structured microtubules (9+0) enclosed by plasma membrane. Housing components of the cell division apparatus between cell divisions, primary cilia also serve as specialized compartments for calcium signaling and hedgehog signaling pathways. Specialized sensory cilia such as retinal photoreceptors and olfactory cilia use diverse ion channels. An ion current has been measured from primary cilia of kidney cells, but the responsible genes have not been identified. The polycystin proteins (PC and PKD), identified in linkage studies of polycystic kidney disease, are candidate channels divided into two structural classes 11-transmembrane proteins (PKD1, PKD1L1 and PKD1L2) remarkable for a large extracellular amino terminus of putative cell adhesion domains and a G-protein-coupled receptor proteolytic site, and the 6-transmembrane channel proteins (PKD2, PKD2L1 and PKD2L2; TRPPs). Evidence indicates that the PKD1 proteins associate with the PKD2 proteins via coiled-coil domains. Here we use a transgenic mouse in which only cilia express a fluorophore and use it to record directly from primary cilia, and demonstrate that PKD1L1 and PKD2L1 form ion channels at high densities in several cell types. In conjunction with an accompanying manuscript, we show that the PKD1L1-PKD2L1 heteromeric channel establishes the cilia as a unique calcium compartment within cells that modulates established hedgehog pathways.
Stream response to precipitation variability: a spectral view based on analysis and modelling of hydrological cycle components
Authors: Markovic D. , Koch M. 
Published: July 2014

AbstractHydrological processes commonly exhibit long‐term persistence, also known as the ‘Hurst phenomenon’. Here, we examine long‐term precipitation and streamflow time series from the Elbe River Basin to quantify differences in the spectral properties and in the Hurst parameter estimates () of the individual hydrological cycle components. Precipitation‐runoff modelling is performed for the Elbe River sub‐catchment Striegis using the Soil and Water Assessment Tool (SWAT). For 38 daily 50 years long streamflow time series from the Elbe River Basin, baseflow separation and spectral analysis is performed. The results show a spectral shift towards low‐frequency scales (>2 years) from precipitation to baseflow, with a parallel increase of from 0.52 (precipitation) to 0.65 (baseflow). The SWAT model is able to reproduce both, the main low‐frequency mode (≈7 yr.) and the (0.62) of the observed Striegis River flow time series. The baseflow appears to be the main component which shapes the low‐frequency response and of streamflow in the Elbe River Basin to the input precipitation. This conclusion is further confirmed through PMWIN‐MODFLOW groundwater modelling of a hypothetic phreatic stream‐connected aquifer system that consists of various soils (sand, loamy sand and silt). A power shift towards lower frequencies and an increase of for the hydraulic heads is obtained, as the aquifer's lateral dimensions increase and its hydraulic conductivity decreases. The average of the groundwater heads is 0.80, 0.90 and 1.0 for sand, loamy sand and silt aquifers, respectively. Copyright © 2014 John Wiley & Sons, Ltd.
Preparation and tribological properties of surface‐modified ZnS nanoparticles
Authors: Wang Libo , Gao Yupeng , Li Zhengyang , Zhou Aiguo , Li Ping 
Published: July 2014

AbstractSurface‐modified ZnS nanoparticles have been fabricated, and the morphologies and crystalline structures of the powder have been characterised by transmission electron microscopy, X‐ray diffraction and Fourier transformation infrared spectrum. The tribological properties of the surface‐modified ZnS (SM‐ZnS) nanoparticles as an additive in PEG400 were evaluated with a four‐ball tester. It was found that the as‐prepared SM‐ZnS nanoparticles had a very narrow size distribution, with the average diameter about 5–10 nm. The SM‐ZnS nanoparticles as the additive led to an obvious improvement in the anti‐wear and friction‐reduction properties of the synthetic PEG400. Analysis indicated that a boundary film was formed during the friction process. Copyright © 2014 John Wiley & Sons, Ltd.
New maximum entropy methods for modeling lifetime distributions
Authors: Asadi Majid , Ebrahimi Nader , Soofi Ehsan S. , Zarezadeh Somayeh 
Published: July 2014

AbstractThis article introduces two new maximum entropy (ME) methods for modeling the distribution of time to an event. One method is within the classical ME framework and provides characterizations of change point models such as the piecewise exponential distribution. The second method uses the entropy of the equilibrium distribution (ED) for the objective function and provides new characterizations of the exponential, Weibull, Pareto, and uniform distributions. With the same moment constraints, the classical ME and the maximum ED entropy algorithms generate different models for the interarrival time. © 2014 Wiley Periodicals, Inc. Naval Research Logistics 61: 427–434, 2014
Boveri at 100: the life and times of Theodor Boveri
Authors: Dietel Manfred 
Published: July 2014

AbstractThis perspective focuses on the life and personality of TH Boveri, who was one of the leading creative and visionary scientists of the second half of the nineteenth century. Born in Bamberg in 1862, he made his scientific career in Munich and Würzburg, where he produced his prolific and important research, including seminal papers on cytogenetics. Of particular note is his work on chromosomal structures and function, including a theory of meiosis, a field almost new at that time. From these studies he created a theoretical model on oncogenesis, Zur Frage der Entstehung maligner Tumoren, which was originally published in 1914. Boveri's personality was characterized by an active and sometimes turbulent temperament, which nevertheless was controlled by scientific objectivity and doubts about his own abilities, at least with regard to his research. These characteristics made him an outstanding scientist who contributed new knowledge to the world of biology and pathology. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd
Structural and functional analysis show that the Escherichia coli uncharacterized protein YjcS is likely an alkylsulfatase
Authors: Liang Yajing , Gao Zengqiang , Dong Yuhui , Liu Quansheng 
Published: July 2014

AbstractSodium dodecyl sulfate (SDS) is a widely used anionic surfactant in industry and research settings, and is known to have a detrimental effect to the environment. The pathway of SDS degradation by bacteria is initiated by an alkylsulfatase and the oxidized product, 1‐dodecanoic acid, subsequently enters into the β‐oxidation pathway and is used as a carbon source. In this work, we solved the crystal structure of Escherichia coli uncharacterized protein YjcS and identified that it belongs to the Type III alkylsulfatase with a signal peptide (residues 1–29) at the N terminus. YjcS hydrolyzed SDS and the double mutant D184N‐H185A located in the conserved HXHXDH catalytic motif abolished this activity.
RVIP: an indistinguishable approach to scalable network simulation at real time
Authors: Kong Jiejun , Li Tingzhen , Wu Dapeng Oliver 
Published: July 2014

AbstractIn the hybrid simulation research, we investigate a new approach to build software virtual networks (SVNs) that are indistinguishable from their equivalent real live networks (LNs). We define the concept of ‘Network's Interactive Turing Test' based on the similar concept used in the artificial intelligence areas. Our goal is to actualize the interactive and indistinguishable real–virtual interface pair (RVIP) for large‐scale computer network simulations. By RVIP's support, a single SVN is indistinguishable from its equivalent LN. In the entire hybrid system, multiple LNs and multiple SVNs are connected using many RVIPs in an arbitrary topology and at real time. To actualize RVIP, the following necessary conditions must be satisfied: (i) the performance of the underlying simulation platform must be faster than real time; (ii) all needed changes incurred by introducing any SVN into an LN scenario are put on the simulation's side. To interact with an SVN, RVIP requires that no change is made on any live node; (iii) an SVN does not exchange simulation events with LNs, that is, only standard IP protocol interactions between SVN and LN are allowed. (iv) Any LN can be dynamically plugged into the hybrid scenario at real time, just like being plugged into an equivalent purely LN. Compared with existing hybrid simulation efforts on NS‐3, QualNet's EXata and OPNET's system‐in‐the‐loop, in this paper, we use the actual RVIP implementation to show that RVIP is a better candidate to pass the Network's Interactive Turing Test owing to the following two advantages: (i) an interactive network tester can easily distinguish the existing hybrid networks from the LNs by using a live topology that cannot be simulated, for example, by including the entire live Internet. But RVIP is not vulnerable to such tests. RVIP can support hybrid scenarios with multiple SVNs and multiple LNs connected by an arbitrary network topology, and with the LNs on and off at anytime. (ii) Performance‐wise, our studies show that RVIP provides more efficient support in terms of common metrics such as larger throughput limit and smaller extra latency; thus, the simulated SVNs are more indistinguishable from their live counterparts. Copyright © 2014 John Wiley & Sons, Ltd.
A node division location detection scheme for chain‐type wireless sensor networks
Authors: Chen Guangzhu , Bao Jiusheng , Zhang Lei 
Published: July 2014

AbstractAs a special type of wireless sensor network, the chain‐type wireless sensor networks can be used to monitor narrow and long regions, such as roads, underground mine tunnels, rivers, and bridges. In this study, a perpendicular bisector division (PB) method was first presented, in which the location may be divided into more location sub‐areas by a perpendicular bisector of each of two location nodes. Compared with the triangulation division method in Approximate Point‐in‐Triangulation Test (APIT), the computable complexity of PB is lower, and the number of division areas is larger. Furthermore, in order to locate targets under rare location nodes, a virtual location node‐perpendicular bisector division (VPB) was presented by a virtual location node based on the geographic shape of the monitored area. Virtual location nodes increase the density of location nodes, which can improve the accuracy of the location in the location algorithm. Second, two range‐free location algorithms were proposed: the location algorithm based on PB (LAPB) and the location algorithm based on VPB (LAVPB). In the end, the location errors performance of APIT, LAPB, and LAVPB for locating miners in an underground mine tunnel was tested. The results show that LAPB and LAVPB have higher location accuracy and are more robust than APIT. LAVPB is more suitable for locating targets in harsh environments. Copyright © 2014 John Wiley & Sons, Ltd.
Prediction‐based MAC‐layer sensing in cognitive radio networks
Authors: Zhang Lei , Xie Cihang , Jiang Tao , Shen Junyang , Qi Qi , Meng Dexiang 
Published: July 2014

AbstractWe consider a cognitive radio network which coexists with multiple primary users (PUs) and secondary users (SUs) transmit over time‐varying channels. In this scenario, one problem of the existing work is the poor performances of throughput and fairness due to variances of SUs' channel conditions and PUs' traffic patterns. To solve this problem, we propose a novel prediction‐based MAC‐layer sensing algorithm. In the proposed algorithm, the SUs' channel quality information and the probability of the licensed channel being idle are predicted. Through the earlier predicted information, we schedule the SUs to sense and transmit on different licensed channels. Specifically, multiple significant factors, including network throughput and fairness, are jointly considered in the proposed algorithm. Then, we formulate the prediction‐based sensing scheduling problem as an optimization problem and solve it with the Hungarian algorithm in polynomial time. Simulation results show that the proposed prediction‐based sensing scheduling algorithm could achieve a good tradeoff between network throughput and fairness among SUs. Copyright © 2014 John Wiley & Sons, Ltd.