bluuebunny/crossref_metadata_2025 huggingface dataset:
A two Turbulence Kinetic Energy model as a scale‐adaptive approach to modeling the planetary boundary layer
Authors: Bhattacharya Ritthik , Stevens Bjorn
Published: January 2016

A two Turbulence Kinetic Energy (2TKE) model is developed to address the boundary layer “grey zone” problem. The model combines ideas from local and nonlocal models into a single energetically consistent framework. By applying the Reynolds averaging to the large eddy simulation (LES) equations that employ Deardorff's subgrid TKE, we arrive at a system of equations for the boundary layer quantities and two turbulence kinetic energies: one which encapsulates the TKE of large boundary‐layer‐scale eddies and another which represents the energy of eddies subgrid to the vertical grid size of a typical large‐scale model. These two energies are linked via the turbulent cascade of energy from larger to smaller scales and are used to model the mixing in the boundary layer. The model is evaluated for three dry test cases and found to compare favorably to large eddy simulations. The usage of two TKEs for mixing helps reduce the dependency of the model on the vertical grid scale as well as on the free tropospheric stability and facilitates a smoother transition from convective to stable regimes. The usage of two TKEs representing two ranges of scales satisfies the prerequisite for modeling the boundary layer in the “grey zone”: an idea that is explored further in a companion paper.
Cost of riparian buffer zones: A comparison of hydrologically adapted site‐specific riparian buffers with traditional fixed widths
Authors: Tiwari T. , Lundström J. , Kuglerová L. , Laudon H. , Öhman K. , Ågren A. M.
Published: January 2016

Traditional approaches aiming at protecting surface waters from the negative impacts of forestry often focus on retaining fixed width buffer zones around waterways. While this method is relatively simple to design and implement, it has been criticized for ignoring the spatial heterogeneity of biogeochemical processes and biodiversity in the riparian zone. Alternatively, a variable width buffer zone adapted to site‐specific hydrological conditions has been suggested to improve the protection of biogeochemical and ecological functions of the riparian zone. However, little is known about the monetary value of maintaining hydrologically adapted buffer zones compared to the traditionally used fixed width ones. In this study, we created a hydrologically adapted buffer zone by identifying wet areas and groundwater discharge hotspots in the riparian zone. The opportunity cost of the hydrologically adapted riparian buffer zones was then compared to that of the fixed width zones in a meso‐scale boreal catchment to determine the most economical option of designing riparian buffers. The results show that hydrologically adapted buffer zones were cheaper per hectare than the fixed width ones when comparing the total cost. This was because the hydrologically adapted buffers included more wetlands and low productive forest areas than the fixed widths. As such, the hydrologically adapted buffer zones allows more effective protection of the parts of the riparian zones that are ecologically and biogeochemically important and more sensitive to disturbances without forest landowners incurring any additional cost than fixed width buffers.
Children as Earwitnesses: Memory for Emotional Auditory Events
Authors: Burrell Lisa Victoria , Johnson Miriam Sinkerud , Melinder Annika
Published: January 2016

We examined the influence of age and emotionality of auditory stimuli on long‐term memory for environmental sound events. Sixty children aged 7–11 years were presented with two environmental sound events: an emotional car crash and a neutral event, someone brushing their teeth. The sound events comprised six individual environmental sounds, and the participants passively listened to the sound events through a headset. After a two‐week delay, participants performed a cued recall task and a recognition task. Independent of age, children were notably poor at recalling the sound events. Children recalled and recognized significantly more sounds from the emotional sound event than the neutral sound event. Additionally, the older children performed the recall task better than the younger children. The present findings confirm and expand the previously reported superiority of emotional material in memory.Copyright © 2016 John Wiley & Sons, Ltd.
3D Hierarchical Co/CoO‐Graphene‐Carbonized Melamine Foam as a Superior Cathode toward Long‐Life Lithium Oxygen Batteries
Authors: Zhang Peng , Wang Rutao , He Mu , Lang Junwei , Xu Shan , Yan Xingbin
Published: January 2016

Carbon based materials as one promising cathode to accommodate the insoluble and insulating discharge products (Li2O2) for lithium oxygen (Li‐O2) batteries have attracted great attention due to their large energy density store ability compared with the other carbon‐free cathodes. However, the side reaction occurring at carbon/Li2O2 interfaces hinders their large‐scale application in Li‐O2 batteries. Herein, a simple and cost‐effective strategy is developed for the growth of core‐shell‐like Co/CoO nanoparticles on 3D graphene‐wrapped carbon foam using 3D melamine foam as the initial backbone. This unique 3D hierarchical carbonized melamine foam‐graphene‐Co/CoO hybrid (CMF‐G‐Co/CoO) with a continuous conductive network and elastic properties is used as binder‐free oxygen electrode for Li‐O2 batteries. Electrochemical and structural measurements show that a synergistic effect is observed between Co/CoO and graphene, where Li2O2 grows on the Co/CoO surfaces instead of the carbon surfaces at the initial discharge state (500 mAh ), indicating the reduced carbon/Li2O2 interfaces and alleviative side reactions during the electrochemical process. Importantly, the CMF‐G‐Co/CoO electrode can achieve greatly improved cycle life over the electrode without aid of the Co/CoO. Furthermore, it delivers a large capacity of ≈7800 mAh and outstanding rate capability, exhibiting the great potential for the application in Li‐O2 batteries.
Predicting the Self‐Assembly of Superparamagnetic Colloids under Magnetic Fields
Authors: Faraudo Jordi , Andreu Jordi S. , Calero Carles , Camacho Juan
Published: January 2016

Self‐assembly processes are very important in material sciences but are particularly difficult to predict quantitatively. This is the case for particulate magnetic materials in which field‐induced self‐assembly processes are essential. This article describes the recent advances in the development of predictive theoretical tools for the study of directed self‐assembly of superparamagnetic colloids under magnetic fields. A practical view is presented of how to employ the new concepts (derived from thermodynamic theory) to predict the possible assembled structures from the properties of the colloids and thermodynamic conditions. Quantitative prediction of kinetics is also discussed for the cases in which equilibrium theory is not relevant. Finally, an outline of fundamental aspects of the theory is presented.
Improved Second Generation Iron Pincer Complexes for Effective Ester Hydrogenation
Authors: Elangovan Saravanakumar , Wendt Bianca , Topf Christoph , Bachmann Stephan , Scalone Michelangelo , Spannenberg Anke , Jiao Haijun , Baumann Wolfgang , Junge Kathrin , Beller Matthias
Published: January 2016

Hydrogenation of esters to alcohols with a well‐defined iron iPr2PNP pincer complex has been recently reported by us and other groups. We now introduce a novel and sterically less hindered Et2PNP congener that provides superior catalytic activity in the hydrogenation of various carboxylic acid esters and lactones compared to the known complex. Successful hydrogenation proceeds under relatively mild conditions (60 °C) with lower catalyst loadings.

magnified image
Understanding Surface Adhesion in Nature: A Peeling Model
Authors: Gu Zhen , Li Siheng , Zhang Feilong , Wang Shutao
Published: January 2016

Nature often exhibits various interesting and unique adhesive surfaces. The attempt to understand the natural adhesion phenomena can continuously guide the design of artificial adhesive surfaces by proposing simplified models of surface adhesion. Among those models, a peeling model can often effectively reflect the adhesive property between two surfaces during their attachment and detachment processes. In the context, this review summarizes the recent advances about the peeling model in understanding unique adhesive properties on natural and artificial surfaces. It mainly includes four parts: a brief introduction to natural surface adhesion, the theoretical basis and progress of the peeling model, application of the peeling model, and finally, conclusions. It is believed that this review is helpful to various fields, such as surface engineering, biomedicine, microelectronics, and so on.
Actuator stiction compensation via model predictive control for nonlinear processes
Authors: Durand Helen , Christofides Panagiotis D.
Published: January 2016

The problem of valve stiction is addressed, which is a nonlinear friction phenomenon that causes poor performance of control loops in the process industries. A model predictive control (MPC) stiction compensation formulation is developed including detailed dynamics for a sticky valve and additional constraints on the input rate of change and actuation magnitude to reduce control loop performance degradation and to prevent the MPC from requesting physically unrealistic control actions due to stiction. Although developed with a focus on stiction, the MPC‐based compensation method presented is general and has potential to compensate for other nonlinear valve dynamics which have some similarities to those caused by stiction. Feasibility and closed‐loop stability of the proposed MPC formulation are proven for a sufficiently small sampling period when Lyapunov‐based constraints are incorporated. Using a chemical process example with an economic model predictive controller (EMPC), the selection of appropriate constraints for the proposed method is demonstrated. The example verified the incorporation of the stiction dynamics and actuation magnitude constraints in the EMPC causes it to select set‐points that the valve output can reach and causes the operating constraints to be met. © 2016 American Institute of Chemical Engineers AIChE J, 62: 2004–2023, 2016
Prognostic impact of persistent cytogenetic abnormalities at complete remission in adult patients with acute lymphoblastic leukemia
Authors: Short Nicholas J. , Kantarjian Hagop M. , Jabbour Elias J. , O'Brien Susan M. , Faderl Stefan , Burger Jan A. , Garris Rebecca , Qiao Wei , Huang Xuelin , Jain Nitin , Konopleva Marina , Kadia Tapan M. , Daver Naval , Borthakur Gautam , Cortes Jorge E. , Ravandi Farhad
Published: January 2016

In acute myelogenous leukemia, the persistent detection of abnormal cytogenetics at complete remission (ACCR) is associated with inferior outcomes. However, the prognostic significance of ACCR in adult patients with acute lymphoblastic leukemia (ALL) is unknown. We evaluated 272 adult patients with ALL and abnormal cytogenetics at baseline who were treated with frontline induction chemotherapy, achieved complete remission (CR) and had cytogenetic analysis performed at the time of CR. ACCR was observed in 26 patients (9.6%). Median relapse‐free survival was 22 months (95% CI, 12 months to not reached) for patients with ACCR vs. 48 months (range, 30–125 months) in patients with normal cytogenetics at CR (NCCR; P = 0.31). Median overall survival also did not differ significantly between the ACCR (99 months [range, 17 months to not reached]) and NCCR groups (67 months [range, 47 months to not reached], P = 0.86). The specificity of ACCR for minimal residual disease (MRD) positivity by multi‐parameter flow cytometry (MFC) was 43%, and there was overall poor correlation between these two methods for the detection of residual disease. When patients were stratified by MRD status, the presence or absence of persistent cytogenetic abnormalities at CR did not add additional prognostic information. This study suggests that there is poor association between MRD assessment by MFC and the presence or absence of cytogenetic abnormalities at CR in adult patients with ALL. ACCR was not associated with adverse outcomes in ALL and did not add additional prognostic information when MRD status by MFC was known. Am. J. Hematol. 91:385–389, 2016. © 2016 Wiley Periodicals, Inc.
Reduced morning cortisol concentration in saliva was associated with obesity: Evidence from community‐dwelling adults in papua new guinea
Authors: Morita Ayako , Natsuhara Kazumi , Vengiau Gwendalyn , Chia‐Jung Chen Cindy , Odani Shingo , Inaoka Tsukasa , Tadokoro Kiyoshi , Suda Kazuhiro , Furusawa Takuro , Siba Peter , Phuanukoonnon Suparat , Umezaki Masahiro
Published: January 2016

Objectives

This study investigated morning salivary cortisol concentration in relation to total body fat composition among community‐dwelling Papua New Guinean adults.

Methods

In addition to demographic and anthropometric measurements, saliva was collected in a single morning from 478 residents in Eastern Highlands Province and Madang Province.

Results

After adjusting for age, region, and occupation, the morning salivary cortisol concentration was significantly negatively correlated with body mass index among men (B = −0.01, P < 0.05) and women (B = −0.013, P < 0.05), and waist circumference (B = −0.007, P < 0.05), waist‐to‐hip‐ratio (B = −1.214, P < 0.05), and subscapular‐to‐triceps skinfold‐thickness ratio (B = −0.045, P < 0.05) among men. Men with total or abdominal body fat mass known for elevated risk of non‐communicable diseases displayed lower cortisol compared to men without such risk.

Conclusions

Papua New Guinean adults with increased accumulation of body fat showed reduced cortisol concentration in morning saliva. Am. J. Hum. Biol. 28:587–590, 2016. © 2016 Wiley Periodicals, Inc.
Photochemical Reduction of Low Concentrations of CO2 in a Porous Coordination Polymer with a Ruthenium(II)–CO Complex
Authors: Kajiwara Takashi , Fujii Machiko , Tsujimoto Masahiko , Kobayashi Katsuaki , Higuchi Masakazu , Tanaka Koji , Kitagawa Susumu
Published: January 2016

Direct use of low pressures of CO2 as a C1 source without concentration from gas mixtures is of great interest from an energy‐saving viewpoint. Porous heterogeneous catalysts containing both adsorption and catalytically active sites are promising candidates for such applications. Here, we report a porous coordination polymer (PCP)‐based catalyst, PCP‐RuII composite, bearing a RuII‐CO complex active for CO2 reduction. The PCP‐RuII composite showed improved CO2 adsorption behavior at ambient temperature. In the photochemical reduction of CO2 the PCP‐RuII composite produced CO, HCOOH, and H2. Catalytic activity was comparable with the corresponding homogeneous RuII catalyst and ranks among the highest of known PCP‐based catalysts. Furthermore, catalytic activity was maintained even under a 5 % CO2/Ar gas mixture, revealing a synergistic effect between the adsorption and catalytically active sites within the PCP‐RuII composite.
SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition
Authors: Chen Bin , LeBlanc Regan , Dayie T. Kwaku
Published: January 2016

Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From 13C and 1H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg2+ (0–0.5 mm)‐bound apo SAM‐II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1′,C1′) chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg2+ will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.
Ultrathin Free‐Standing Ternary‐Alloy Nanosheets
Authors: Hong Jong Wook , Kim Yena , Wi Dae Han , Lee Seunghoon , Lee Su‐Un , Lee Young Wook , Choi Sang‐Il , Han Sang Woo
Published: January 2016

A synthesis strategy for the preparation of ultrathin free‐standing ternary‐alloy nanosheets is reported. Ultrathin Pd‐Pt‐Ag nanosheets with a thickness of approximately 3 nm were successfully prepared by co‐reduction of the metal precursors in an appropriate molar ratio in the presence of CO. Both the presence of CO and the interplay between the constituent metals provide fine control over the anisotropic two‐dimensional growth of the ternary‐alloy nanostructure. The prepared Pd‐Pt‐Ag nanosheets were superior catalysts of ethanol electrooxidation owing to their specific structural and compositional characteristics. This approach will pave the way for the design of multicomponent 2D nanomaterials with unprecedented functions.
C−C Bond‐Forming Strategy by Manganese‐Catalyzed Oxidative Ring‐Opening Cyanation and Ethynylation of Cyclobutanol Derivatives
Authors: Ren Rongguo , Wu Zhen , Xu Yan , Zhu Chen
Published: January 2016

A novel C−C bond‐forming strategy employing manganese‐catalyzed ring‐opening of cyclobutanol substrates, followed by cyanation or ethynylation, is described. A cyano C1 unit and ethynyl C2 unit are regiospecifically introduced to the γ‐position of ketones at room temperature, providing a mild yet powerful method for production of elusive aliphatic nitriles and alkynes. All transformations described are based on a common sequence: 1) oxidative ring‐opening of cyclobutanol substrates by C−C bond cleavage; 2) radical addition to triple bonds bearing an arylsulfonyl group; and 3) radical‐mediated C−S bond cleavage.
Ca2+‐Induced Oxygen Generation by FeO42− at pH 9–10
Authors: Ma Li , Lam William W. Y. , Lo Po‐Kam , Lau Kai‐Chung , Lau Tai‐Chu
Published: January 2016

Although FeO42− (ferrate(IV)) is a very strong oxidant that readily oxidizes water in acidic medium, at pH 9–10 it is relatively stable (<2 % decomposition after 1 h at 298 K). However, FeO42− is readily activated by Ca2+ at pH 9–10 to generate O2. The reaction has the following rate law: d[O2]/dt=kCa[Ca2+][FeO42−]2. 18O‐labeling experiments show that both O atoms in O2 come from FeO42−. These results together with DFT calculations suggest that the function of Ca2+ is to facilitate O–O coupling between two FeO42‐ions by bridging them together. Similar activating effects are also observed with Mg2+ and Sr2+.
Two novel peptides with angiotensin I converting enzyme inhibitory and antioxidative activities from Scorpaena notata muscle protein hydrolysate
Authors: Aissaoui Neyssene , Abidi Ferid , Hardouin Julie , Abdelkafi Zaineb , Marrakchi Naziha , Jouenne Thierry , Marzouki M. Nejib
Published: January 2016

Fish protein hydrolysate was prepared from muscle of small red scorpionfish (Scorpaena notata) by treatment with a protease from the fungus Penicillium digitatum. Protein hydrolysate was found to strongly inhibit the angiotensin I converting enzyme and exhibited high antioxidative activity through 1,1‐diphenyl‐2‐picrylhydrazyl free radical scavenging assay. After ultrafiltration, peptides were isolated by a two‐step procedure: size exclusion chromatography on a Toyopearl HW‐40 followed by reversed‐phase high‐performance liquid chromatography with a high purification yield of 2.5 mg of peptide per gram of initial protein. Two major peptides were then identified by nanoscale liquid chromatography coupled to tandem mass spectrometry (nano‐LC‐MS/MS), corresponding to the following sequences: Leu‐Val‐Thr‐Gly‐Asp‐Asp‐Lys‐Thr‐Asn‐Leu‐Lys (1,204.665 Da) and Asp‐Thr‐Gly‐Ser‐Asp‐Lys‐Lys‐Gln‐Leu (992.511 Da). These peptides, mainly composed of hydrophilic amino acids, showed high antioxidative and angiotensin I converting enzyme inhibitory activities. These data suggest that the two novel peptides isolated from the muscle hydrolysate of small red scorpionfish can be a beneficial ingredient for functional foods or pharmaceuticals against hypertension and oxidative stress.
Multiomics approach to identify novel biomarkers for dilated cardiomyopathy: Proteome and transcriptome analyses of 4C30 dilated cardiomyopathy mouse model
Authors: Nishigori Mitsuhiro , Yagi Hiroaki , Mochiduki Akikazu , Minamino Naoto
Published: January 2016

Dilated cardiomyopathy (DCM) is an intractable disease, without any radical treatment option other than cardiac transplantation. Additionally, biomarkers to determine progressive staging are not yet available. Irrespective of the diversity of causative gene mutations, the phenotype of DCM is rather common. Therefore, it is plausible to determine DCM staging in terms of variations in protein and mRNA levels. In this study, we performed proteome and transcriptome analysis of the left ventricle of 4C30 DCM model mice showing mild and severe phenotypes at 12 and 24 weeks (wk) after birth, respectively. Proteomic analyses results showed 109 proteins that increased and 133 others that decreased among 1874 detected proteins. We selected biomarker candidates by confirming consistent alterations in protein levels at 12 and 24 wk, and mRNA levels at 12 wk, and narrowed these down based on the requirement that they should be detectable in blood. Finally, we selected six biomarker candidates based on sustained or augmented alteration at 24 wk and confirmed their definite alterations in the left ventricle by quantitative polymerase chain reaction, western blot analysis, and multiple reaction monitoring (MRM). To assess the validity of this strategy, we measured plasma concentrations of the six candidates by MRM method and identified two proteins (FTL1 and GRP78) that demonstrated significant elevation in the 4C30 mice plasma. Taken together, a multiomics strategy comparing tissue expression levels of proteins and mRNAs between diseased and control groups, with appropriate confirmation, is a promising approach for the discovery of new biomarkers. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 491–502, 2016.
Intrinsic Förster Resonance Energy Transfer Imaging Technique for Detection of Native Protein in Live Cells
Authors: Lee Hanki , Kang Hyo Jin , Kim Ju Hwan , Lee Eun Seong , Chung Sang J.
Published: January 2016

To detect a native target protein and its interaction with drugs in live cells, we developed an intrinsic fluorescence resonance energy transfer (iFRET) imaging technique (iFIT). TheiFITemploys a target‐specific fluorescent probe in combination with a deepUVbiological microscope. TheiFRETutilizes tryptophan residues of the target protein and a cell‐permeable target‐specific probe, which is selectively excited by the intrinsic tryptophan fluorescence (λem= 350 nm), asFRETdonors and acceptors, respectively. As the Förster distance between the tryptophan residues and theiFITprobe is about 2 nm, aniFRETsignal is generated by specific interaction of the target protein and the selectiveiFITprobe. A deepUVbiological microscope equipped with a quartz objective and two optical filters (288 and 365 nm) on a shutter was constructed to facilitate the detection of theiFRETsignal upon binding of the probe to its target, in live cells. We successfully achieved imaging of native streptavidin in live cells with the thus developediFIT, after simple treatment of live cells with the correspondingiFITprobes.
A New Series of Cycloalkane‐fused Coumarin Sulfonates: Synthesis and In Vitro Antiproliferative Screening
Authors: El‐Gamal Mohammed I. , Baek Daejin , Oh Chang‐Hyun
Published: January 2016

In this paper, we report the synthesis of 14 new cycloalkane‐fused tricyclic coumarin sulfonate derivatives. They were examined for in vitro anticancer activity against NCI‐57 cancer cell line panel of nine different cancer types. Among all the target analogs, compounds 1c, 1e, and 1n showed the highest activities. Compound 1e exerted the highest percentage growth inhibition (91.91%) against SNB‐75 CNS cancer cell line at 10 μM concentration and was more active than carmustine against this cell line. Compound 1c also showed strong activity against HT29 colon, ACHN renal, and PC‐3 prostate cancer cell lines. Furthermore, compound 1n was selective toward the HT29 colon cancer cell line. Compounds 1c, 1e, and 1n showed superior selectivity against cancer cell lines compared to the noncancerous RAW 264.7 macrophages. The in silico predictions estimate the oral bioavailability, which is in compliance with Lipinski's rule of five.
Serum midkine as a biomarker for malignancy, prognosis, and chemosensitivity in head and neck squamous cell carcinoma
Authors: Yamashita Taku , Shimada Hideaki , Tanaka Shingo , Araki Koji , Tomifuji Masayuki , Mizokami Daisuke , Tanaka Nobuaki , Kamide Daisuke , Miyagawa Yoshihiro , Suzuki Hiroshi , Tanaka Yuya , Shiotani Akihiro
Published: January 2016

Improved therapies for individuals with head and neck squamous cell carcinoma (HNSCC) may be developed by identification of appropriate biomarkers. The aim of this study was to evaluate the usefulness of serum midkine measurement as a biomarker for HNSCC. Pretreatment serum midkine concentrations were measured in 103 patients with HNSCC and 116 control individuals by enzyme‐linked immunosorbent assay. Midkine expression in tumor tissues from 33 patients with HNSCC who underwent definitive surgical resection without preoperative treatment was examined by immunohistochemistry. The cut‐off serum midkine concentrations for predicting the presence of head and neck malignancy and chemosensitivity to induction chemotherapy, as determined using receiver operating characteristic curves, were 482 and 626 pg/mL, respectively. Spearman bivariate correlations showed positive correlations between serum midkine levels and immunohistochemistry staining score (r = 0.612, P < 0.001). The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of serum midkine concentration for detection of HNSCC were 57.3, 85.3, 77.6, 69.2, and 72.1%, respectively. However, for predicting the response to induction chemotherapy, the values were 84.6, 60.9, 71.0, 77.8, and 73.5%, respectively. Serum midkine concentration was identified as an independent prognostic factor by multivariate analysis, using Cox's proportional hazards model (P = 0.027). Overexpression of serum midkine yielded a relative risk of death of 3.77, with 95% confidence limits ranging from 1.15 to 17.0. Serum midkine levels in patients with HNSCC were associated with malignancy, chemosensitivity, and prognosis. Serum midkine may be a useful, minimally invasive biomarker for early detection, therapeutic decision‐making, and predicting prognosis.
Pretreatment serum interleukin‐1β, interleukin‐6, and tumor necrosis factor‐α levels predict the progression of colorectal cancer
Authors: Chang Pei‐Hung , Pan Yi‐Ping , Fan Chung‐Wei , Tseng Wen‐Ko , Huang Jen‐Seng , Wu Tsung‐Han , Chou Wen‐Chi , Wang Cheng‐Hsu , Yeh Kun‐Yun
Published: January 2016

The correlations of pretreatment serum concentrations of proinflammatory cytokines such as interleukin (IL)‐1β, IL‐6, and tumor necrosis factor‐α (TNFα) with the clinicopathologic features and progression of colorectal cancer (CRC) were investigated. The pretreatment serum levels of IL‐1β, IL‐6, and TNFα were measured in 164 CRC patients before treatment. The relationships between changes in proinflammatory cytokine and C‐reactive protein (CRP) levels and both clinicopathologic variables and disease progression were examined by univariate and multivariate analysis. Advanced tumor stage was associated with a poorer histologic differentiation, higher CRP level, lower albumin level, and inferior progression‐free survival rate (PFSR). Furthermore, high levels of CRP (>5 mg/L) were associated with proinflammatory cytokine intensity, defined according to the number of proinflammatory cytokines with levels above the median level (IL‐1β ≥10 pg/mL; IL‐6 ≥ 10 pg/mL; and TNFα ≥55 pg/mL). Under different inflammation states, proinflammatory cytokine intensity, in addition to tumor stage, independently predicted PFSR in patients with CRP <5 mg/L, whereas tumor stage was the only independent predictor of PFSR in patients with CRP ≥5 mg/L. Proinflammatory cytokine intensity and the CRP level are clinically relevant for CRC progression. Measurement of IL‐1β, IL‐6, and TNFα serum levels may help identify early cancer progression among patients with CRP <5 mg/L in routine practice.
Enantioselective Oxidative Rearrangements with Chiral Hypervalent Iodine Reagents
Authors: Brown Michael , Kumar Ravi , Rehbein Julia , Wirth Thomas
Published: January 2016

A stereoselective hypervalent iodine‐promoted oxidative rearrangement of 1,1‐disubstituted alkenes has been developed. This practically simple protocol provides access to enantioenriched α‐arylated ketones without the use of transition metals from readily accessible alkenes.
Work stealing with private integer–vector–matrix data structure for multi‐core branch‐and‐bound algorithms
Authors: Gmys Jan , Leroy Rudi , Mezmaz Mohand , Melab Nouredine , Tuyttens Daniel
Published: January 2016

In this paper, the focus is put on multi‐core branch‐and‐bound algorithms for solving large‐scale permutation‐based optimization problems. We investigate five work stealing (WS) strategies with a new data structure called integer–vector–matrix (IVM). In these strategies, each thread has a private IVM allowing the local management of a set of subproblems enumerated using a factorial system. The WS strategies differ in the way the victim thread is selected and the granularity of stolen work units (intervals of factoradics). To assess the efficiency of the private IVM‐based WS approach, the five WS strategies have been extensively experimented on the flowshop scheduling permutation problem and compared with their conventional linked‐list‐based counterparts. The obtained results demonstrate that the IVM‐based WS outperforms the linked‐list‐based one in terms of CPU time, memory usage and number of performed WS operations. Copyright © 2016 John Wiley & Sons, Ltd.
Systematic and quantitative assessment of the effect of chronic kidney disease on CYP2D6 and CYP3A4/5
Authors: Yoshida K , Sun B , Zhang L , Zhao P , Abernethy DR , Nolin TD , Rostami‐Hodjegan A , Zineh I , Huang S‐M
Published: January 2016

Recent reviews suggest that chronic kidney disease (CKD) can affect the pharmacokinetics of nonrenally eliminated drugs, but the impact of CKD on individual elimination pathways has not been systematically evaluated. In this study we developed a comprehensive dataset of the effect of CKD on the pharmacokinetics of CYP2D6‐ and CYP3A4/5‐metabolized drugs. Drugs for evaluation were selected based on clinical drug–drug interaction (CYP3A4/5 and CYP2D6) and pharmacogenetic (CYP2D6) studies. Information from dedicated CKD studies was available for 13 and 18 of the CYP2D6 and CYP3A4/5 model drugs, respectively. Analysis of these data suggested that CYP2D6‐mediated clearance is generally decreased in parallel with the severity of CKD. There was no apparent relationship between the severity of CKD and CYP3A4/5‐mediated clearance. The observed elimination‐route dependency in CKD effects between CYP2D6 and CYP3A4/5 may inform the need to conduct clinical CKD studies with nonrenally eliminated drugs for optimal use of drugs in patients with CKD.
Probabilistic query generation and fuzzy c‐means clustering for energy‐efficient operation in wireless sensor networks
Authors: Kumar Pramod , Chaturvedi Ashvini
Published: January 2016

Depending upon sensing attributes, wireless sensor networks (WSNs) are classified as event driven, time driven, and query driven. In a given surveillance area, approximation of query generation process using uniform probability mass function (PMF) model seems to be reasonable in aggregate terms based on observations extracted from lifetime span of WSNs. However, owing to random generation aspects of query and the associated temporal variations, the Poisson distribution‐based model appears to be more appropriate to resemble the realistic query generation pattern. Invariably, in all the sensor network architectures, the energy management requires an important consideration owing to limited energy resources. For the optimal utilization of energy resources, we propose fuzzy c‐means (FCM) algorithm to form clusters in a hierarchical network configuration. Network performance is measured in terms of key performance measures, namely, average residual energy status, critical residual energy status (CRES), and number of network nodes that attain the CRES mark. These performance measures are estimated and analyzed for three different PMF models of query generation namely Uniform, Gaussian and Poisson. The merit of deploying FCM algorithm in terms of maintaining much better energy profile of the entire network is discussed. Copyright © 2016 John Wiley & Sons, Ltd.
The cytopathology of mycobacterial infection
Authors: Michelow Pamela , Omar Tanvier , Field Andrew , Wright Colleen
Published: January 2016

Mycobacterial infection, tuberculosis (TB) in particular, remains one of the world's deadliest communicable diseases in adults and particularly in children, in low and middle income countries. The combination of human immunodeficiency virus (HIV) and TB is often lethal with TB accounting for 25% of deaths in the HIV population.

One of the cornerstones for reducing the TB epidemic is early case detection using high quality diagnostic techniques. Cytology, especially fine needle aspiration biopsy (FNAB) is able to diagnose mycobacterial infection in a rapid and cost‐effective manner without requiring surgery, thus allowing appropriate management to be quickly instituted. Confirmatory ancillary tests can effectively be performed on cytologic material. In this review, the pertinent cytomorphology of mycobacterial infection in various exfoliative and FNAB specimens is presented, in both immunocompetent and immunosuppressed patients. In the immunosuppressed, the typical cytomorphology of caseating granulomatous inflammation may not be seen but suppurative necrotic inflammation, mycobacterial spindle pseudotumour or a specimen comprised entirely of necrosis may be seen instead. This review includes discussion of currently available ancillary tests that can be performed on cytologic specimens. Diagn. Cytopathol. 2016;44:255–262. © 2016 Wiley Periodicals, Inc.
Cytologic diagnosis of coccidioidomycosis: Spectrum of findings in Southern Arizona patients over a 10 year period
Authors: Aly F. Zahra , Millius Rebecca , Sobonya Richard , Aboul‐Nasr Khalid , Klein Robert
Published: January 2016

Background

The largest series examining the cytological diagnosis of coccidioidomycosis was reported more than 20 years ago and only considered fine needle aspiration (FNA) specimens from pulmonary nodules. Since then, there has been a substantial increase in the incidence of the disease in endemic regions. The aims of this study were to examine the spectrum of Coccidioides in all cytologic specimens and detail their diagnostic and clinical features. The prevalence of infection is also examined against temperature and precipitation data.

Methods

The Department of Pathology database was retrospectively searched for cases diagnosed as coccidioidomycosis. Climate report was obtained from National Weather Service Forecast Office. Statistical analysis was carried out using JMP version 11.2.0.

Results

The presence of Coccidiodes was microscopically diverse with immature spherules, variably sized spherules, endosporulating spherules, empty spherules, and ruptured spherules being observed. Bronchoalveolar lavages demonstrated the greatest number of different forms of Coccidioides and were associated with acute inflammatory response. Granulomas were rare and mostly seen in lymph nodes and extra pulmonary sites. A necrotic background with paucity of inflammation was frequently seen in lung FNA. Immune competent patients outnumbered immunocompromised patients, illustrating the importance of considering the diagnosis in all patients. The reported association between rainfall and peak prevalence was not observed in our study.

Conclusion

Coccidioides has diverse cytological appearance and varied host response depending on the site and type of preparation examined. In endemic areas, the disease should be considered in all patients, independent of immune status, and throughout the year. Diagn. Cytopathol. 2016;44:195–200. © 2016 Wiley Periodicals, Inc.
Effects of fertilization on microbial abundance and emissions of greenhouse gases (CH4 and N2O) in rice paddy fields
Authors: Fan Xianfang , Yu Haiyang , Wu Qinyan , Ma Jing , Xu Hua , Yang Jinghui , Zhuang Yiqing
Published: January 2016

This study is to explore effects of nitrogen application and straw incorporation on abundance of relevant microbes and CH4 and N2O fluxes in a midseason aerated rice paddy field. Fluxes of CH4 and N2O were recorded, and abundance of relevant soil microbial functional genes was determined during rice‐growing season in a 6‐year‐long fertilization experiment field in China. Results indicate that application of urea significantly changed the functional microbial composition, while the influence of straw incorporation was not significant. Application of urea significantly decreased the gene abundances of archaeal amoA and mcrA, but it significantly increased the gene abundances of bacterial amoA. CH4 emission was significantly increased by fresh straw incorporation. Incorporation of burnt straw tended to increase CH4 emission, while the urea application had no obvious effect on CH4 emission. N2O emission was significantly increased by urea application, while fresh or burnt straw incorporation tended to decrease N2O emission. The functional microbial composition did not change significantly over time, although the abundances of pmoA, archaeal amoA, nirS, and nosZ genes changed significantly. The change of CH4 emission showed an inverse trend with the one of the N2O emissions over time. To some extent, the abundance of some functional genes in this study can explain CH4 and N2O emissions. However, the correlation between CH4 and N2O emissions and the abundance of related functional genes was not significant. Environmental factors, such as soil Eh, may be more related to CH4 and N2O emissions.
The use of Hardy–Weinberg Equilibrium in clonal plant systems
Authors: Douhovnikoff Vladimir , Leventhal Matthew
Published: January 2016

Traditionally population genetics precludes the use of the same genetic individual more than once in Hardy–Weinberg (HW) based calculations due to the model's explicit assumptions. However, when applied to clonal plant populations this can be difficult to do, and in some circumstances, it may be ecologically informative to use the ramet as the data unit. In fact, ecologists have varied the definition of the individual from a strict adherence to a single data point per genotype to a more inclusive approach of one data point per ramet. With the advent of molecular tools, the list of facultatively clonal plants and the recognition of their ecological relevance grows. There is an important risk of misinterpretation when HW calculations are applied to a clonal plant not recognized as clonal, as well as when the definition of the individual for those calculations is not clearly stated in a known clonal species. Focusing on heterozygosity values, we investigate cases that demonstrate the extreme range of potential modeling outcomes and describe the different contexts where a particular definition could better meet ecological modeling goals. We emphasize that the HW model can be ecologically relevant when applied to clonal plants, but caution is necessary in how it is used, reported, and interpreted. We propose that in known clonal plants, both genotype (GHet) and ramet (RHet) based calculations are reported to define the full range of potential values and better facilitate cross‐study comparisons.
Quantitative assessment of the functional plasticity of memory CD8+ T cells
Authors: Baz Adriana , Groves Penny , Buttigieg Kathy , Apte Simon H. , Kienzle Norbert , Kelso Anne
Published: January 2016

While the functional plasticity of memory CD4+ T cells has been studied extensively, less is known about this property in memory CD8+ T cells. Here, we report the direct measurement of plasticity by paired daughter analysis of effector and memory OT‐I CD8+ T cells primed in vivo with ovalbumin. Naïve, effector, and memory OT‐I cells were isolated and activated in single‐cell culture; then, after the first division, their daughter cells were transferred to new cultures with and without IL‐4; expression of IFN‐γ and IL‐4 mRNAs was measured 5 days later in the resultant subclones. Approximately 40% of clonogenic memory CD8+ T cells were bipotential in this assay, giving rise to an IL‐4− subclone in the absence of IL‐4 and an IL‐4+ subclone in the presence of IL‐4. The frequency of bipotential cells was lower among memory cells than naïve cells but markedly higher than among 8‐day effectors. Separation based on high or low expression of CD62L, CD122, CD127, or Ly6C did not identify a phenotypic marker of the bipotential cells. Functional plasticity in memory CD8+ T‐cell populations can therefore reflect modulation at the level of a single memory cell and its progeny.
Rare‐Earth Metal Oxo/Hydroxo Clusters – Synthesis, Structures, and Applications
Authors: Wagner Anna T. , Roesky Peter W.
Published: January 2016

Multinuclear rare‐earth metal coordination clusters bridged by oxo/hydroxo units have emerged from being lab curiosities to become a readily accessible class of compounds. New synthetic strategies for accessing these compounds on reasonable scales have been established. Clusters of different sizes have been investigated in terms of their magnetic and photophysical properties. Some preliminary biological applications have also been established.
Synthesis and Dynamic Behavior of Chiral NNO‐Scorpionate Zinc Initiators for the Ring‐Opening Polymerization of Cyclic Esters
Authors: Honrado Manuel , Otero Antonio , Fernández‐Baeza Juan , Sánchez‐Barba Luis F. , Garcés Andrés , Lara‐Sánchez Agustín , Rodríguez Ana M.
Published: January 2016

The reaction of chiral alcohol–scorpionate compounds bpzbeH [bpzbeH = 1,1‐bis(3,5‐dimethylpyrazol‐1‐yl)‐3,3‐dimethyl‐2‐butanol] or bpzteH [bpzteH = 2,2‐bis(3,5‐dimethylpyrazol‐1‐yl)‐1‐para‐tolylethanol] with [ZnR2] (R = Me, Et, CH2SiMe3) in a 1:2 molar ratio afforded the dinuclear chiral zinc alkyls [Zn(R)(κ2‐NNµ‐O)Zn(R)2] (1–4) [κ2‐NNµ‐O = bpzbe, R = Me (1), Et (2), CH2SiMe3 (3); bpzte, R = Et (4)]. Subsequent alcoholysis or thioalcoholysis reaction with ArEH (1 equiv.; E = O, S; Ar = 2,6‐C6H3Me2) yielded the chiral dinuclear mixed alkyl–alryl oxides/thioaryl oxides [(ZnR)2(κN:κN‐µ‐O)(µ‐EAr)] (5–12) [κN:κN‐µ‐O = bpzbe, E = O, R = Me (5), Et (6), CH2SiMe3 (7); bpzte, E = O, R = Et (8); bpzbe, E = S, R = Me (9), Et (10), CH2SiMe3 (11); bpzte, E = S, R = Et (12)]. The alcoholysis reaction of the previously reported monoalkyls [Zn(Me)(κ3‐NNO)] or [Zn(R)(κ‐NNµ‐O)]2 with ArOH (1 equiv., Ar = 2,6‐C6H3Me2) afforded the chiral aryl oxides [Zn(OAr)(κ2‐NNµ‐O)]2 (13–14) [κ2‐NNµ‐O = bpzbe (13); bpzte (14)]. The X‐ray crystal structures of 3, 5, 6, and 14 confirmed a dinuclear structure in all cases with the alkoxide of the heteroscorpionates in a µ‐bridging mode between the ZnII centers. Variable‐temperature NMR spectroscopic studies were carried out to study their dynamic behavior in solution. Complexes 1–9 and 12 can act as single‐component initiators for the ROP of ε‐CL and l‐/rac‐LA, and afforded materials with low molecular weights and narrow monomodal molecular weight distributions. MALDI‐TOF mass spectra confirmed that for 5–8 the initiation occurred through nucleophilic attack by the alkoxide group, rather than the alkyl group, on the lactide monomer. Furthermore, inspection of the kinetic parameters showed propagations with a pseudo‐first‐order dependence on monomer and catalyst concentrations. Microstructural analysis of poly(rac‐lactide) revealed that the mixed alkyl/aryl oxide‐substituted initiators exert a moderate level of heteroselectivity (Ps = 0.66).
Tuning the Basicity of a Metal‐Templated Brønsted Base to Facilitate the Enantioselective Sulfa‐Michael Addition of Aliphatic Thiols to α,β‐Unsaturated N‐Acylpyrazoles
Authors: Ding Xiaobing , Tian Cheng , Hu Ying , Gong Lei , Meggers Eric
Published: January 2016

The enantioselective addition of aliphatic thiols to α,β‐unsaturated N‐acylpyrazoles catalyzed by a bis‐cyclometalated iridium(III) complex with fine‐tuned Brønsted basicity was investigated. Good to excellent yields (71–99 %) and enantioselectivities (86–98 % ee) were achieved at catalyst loadings of 0.2–2.5 mol‐%. In this metal‐templated catalyst design, the metal serves as a structural center and the catalysis is executed by the organic ligand sphere through a combination of proton transfer, hydrogen‐bond formation, and electrostatic interactions.
Back‐arc magma processes in the Okinawa Trough: new insights from textural and compositional variations of plagioclase in basalts
Authors: Lai Zhiqing , Zhao Guangtao , Han Zongzhu , Liu Bo. , Bu Xuejiao , Leng Chuanxu
Published: January 2016

The evolution of magma during ascent through the crust in the region of the Okinawa Trough is recorded by its mineralogy. In this study, we utilized the characteristics of plagioclase minerals in basaltic magma to deduce magma generation processes, by examining (via back‐scattered electron images) the compositional features of plagioclase phenocrysts in basalts dredged from the middle and southern portions of the Okinawa Trough, which provided a detailed account of the evolution and crystallization of the magma. The crystallization and evolutionary histories of magmas from the middle Okinawa Trough are distinct from those in the southern Okinawa Trough. In the middle Okinawa Trough, we identified seven textural varieties of plagioclase: homogeneous‐core, fine oscillatory‐zoned, core‐sieved, mantle‐sieved, patchy‐core, glomerocrystic and microlitic. Anorthite (An) contents in the cores of plagioclase crystals are 80–87%, while concentrations of Fe, Mg and Sr vary more strongly, especially in patchy‐core plagioclase. The homogeneous‐core, fine oscillatory‐zoned and glomerocrystic plagioclase crystallized in deep‐seated chambers. In contrast, the core‐sieved, mantle‐sieved and patchy‐core textures developed when magmas ascended slowly and were injected into shallow chambers, during which plagioclase was resorbed and dissolved due to decompression. In the southern Okinawa Trough, homogeneous‐core plagioclase crystallized when magma ascended rapidly through deep conduits and was injected into a shallow chamber; under these conditions, only homogeneous‐core and core‐sieved plagioclase phenocrysts crystallized in the shallow chamber. The core of homogeneous‐core plagioclase (An86–An93) was partially resorbed and contaminated by crustal material. Degassing and undercooling promoted the rapid crystallization of microlitic plagioclase, especially in the outermost rims, during and after the extraction of magma from shallow chambers, in both the middle and southern Okinawa Trough. Copyright © 2016 John Wiley & Sons, Ltd.